Structure-Function Analysis of the rgh3 Splicing Factor in Maize


Material Information

Structure-Function Analysis of the rgh3 Splicing Factor in Maize
Physical Description:
1 online resource (112 p.)
Martin, Federico
University of Florida
Place of Publication:
Gainesville, Fla.
Publication Date:

Thesis/Dissertation Information

Doctorate ( Ph.D.)
Degree Grantor:
University of Florida
Degree Disciplines:
Plant Molecular and Cellular Biology
Committee Chair:
Settles, Andrew M
Committee Members:
Cline, Kenneth C
Rathinasabapathi, Bala
Chase, Christine D
Condit, Richard C


Subjects / Keywords:
alternativesplicing -- hypomorphic -- maize -- rgh3
Plant Molecular and Cellular Biology -- Dissertations, Academic -- UF
Plant Molecular and Cellular Biology thesis, Ph.D.
bibliography   ( marcgt )
theses   ( marcgt )
government publication (state, provincial, terriorial, dependent)   ( marcgt )
born-digital   ( sobekcm )
Electronic Thesis or Dissertation


Alternative RNA splicing produces multiple mRNA species from individual genes increasing protein diversity and regulating gene expression. Genome sequencing project shave shown that about 42% to 45% of intron-containing genes in plants are alternatively spliced, but little is known about how alternative splicing is controlled. The rough endosperm3 (rgh3) mutant causes developmental defects that are either seed or seedling lethal. Rgh3 encodes a U2AF35 related protein (URP), which is apredicted RNA splicing factor. U2AF35 proteins identify splice acceptor sites during RNA processing and function through protein-protein interactions by creating complexes with U2AF65 and other Serine/Argininerich-proteins (SR-proteins). Semi-quantitative RT-PCR analyses of alternatively spliced genes showed that rgh3affects splicing in a subset of genes supporting a role for RGH3 in alternative splicing. Rgh3 is alternatively spliced, producing at least 19 different spliced variants. Interestingly, only one variant is predicted to encode a full-length URP ortholog containing anN-terminal acidic domain followed by two zinc fingers (Zn) flanking a U2AFhomology motif (UHM) domain and a C-terminal RS-like domain. Several Rgh3 splice variants produce truncated proteins missing one to several domains. GFP fused to full-length RGH3localized to the nucleolus and nuclear speckles. Functional analysis with the endogenous truncated protein variants and an artificial deletion of the UHM domain fused to GFP showed that while the acidic domain contains a nuclear localization signal, the RS-like domain enhances nuclear localization and isalso important for protein recruitment to nuclear speckles. The UHM domain is a modified RRM domain that allows protein-protein interaction and in RGH3 it enables interaction with U2AF65. These results suggest that RGH3 participates in the U2-type spliceosome and its function is regulated by alternative splicing creating truncated variants that render the protein unstable and excluded from the spliceosome.
General Note:
In the series University of Florida Digital Collections.
General Note:
Includes vita.
Includes bibliographical references.
Source of Description:
Description based on online resource; title from PDF title page.
Source of Description:
This bibliographic record is available under the Creative Commons CC0 public domain dedication. The University of Florida Libraries, as creator of this bibliographic record, has waived all rights to it worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.
Statement of Responsibility:
by Federico Martin.
Thesis (Ph.D.)--University of Florida, 2012.
Adviser: Settles, Andrew M.
Electronic Access:

Record Information

Source Institution:
Rights Management:
Applicable rights reserved.
lcc - LD1780 2012
System ID:

This item is only available as the following downloads:

Full Text




2 2012 Federico Martin


3 To my parents and siblings


4 ACKNOWLEDGMENTS I would first like to thank my parents, Oscar and Ana, and my siblings Santiago, Ma. Eugenia, Ma. Cecil ia, Ignacio and Ma. Soledad for their tremendous support and unconditional love. They are in great part the reason I am here writing this document. I would really like to thank my advisor Dr. A. Mark Settles for patiently guiding me from beginning to end and for challenging me to become a much broader scientist. I also thank my committee membe rs Dr. Christine Chase, Dr. Kenneth Cline, Dr. Richard Condit, and Dr. Bala Rathinasabapathi for their guidance and suggestions. I extend my gratitude to the members of the P lant M olecular and C ellular B iology (PMCB) program for their support, and to all current and former students who have been great partners and friends. I truly need to parti cularly to Dr. Diego Fajardo, Dr. Romain Fouquet and Christy Gault for all their help and guidance with this project. I also include Dr. Chi Wah Tseung, Dr. Gertie Spielbauer, Dr. Jeff Gustin, John Baier, Joe Black, Diana Grigalba, Alyssa Baggadion, Tyler Polich t and Sarah Dai ley for their great companionship and support. F inally, I specially thank my friends Carlos, Claudia, Jose, Cynnamon, Eugenia, Andres, Belen, Gabriela, Patan, Florencia, Pablo, Paola, Guy Raul, Mike and to all of those who have supported me in all my scientific and life end eavors and with whom I have shared countless moments of enjoyment that will never be forgotten. Gracias total e s.


5 TABLE OF CONTENTS page ACKNOWLEDGMENTS ................................ ................................ ................................ .. 4 LIST OF TABLES ................................ ................................ ................................ ............ 7 LIST OF FIGURES ................................ ................................ ................................ .......... 8 LIST OF ABBREVIATIONS ................................ ................................ ............................. 9 ABSTRACT ................................ ................................ ................................ ................... 10 CHAPTER 1 INTRODUCTION ................................ ................................ ................................ .... 12 The Spliceosome and the Splicing Reaction ................................ ........................... 12 Alternative Splicing and Gene Regulation ................................ ............................... 15 The U2AF Splicing Complex ................................ ................................ ................... 17 The U2AF 35 Related Protein (URP) ................................ ................................ ........ 19 2 ALTERNATIVE SPLICING PRODUCES RGH3 PROTEIN ISOFORMS WITH DIFFERENT FUNCTIONS ................................ ................................ ...................... 21 Introduction ................................ ................................ ................................ ............. 21 Results ................................ ................................ ................................ .................... 23 The Rgh3 Transcript is Alternative Spliced ................................ ....................... 23 Protein Coding Potential of Rgh3 Transcript Isoforms ................................ ...... 25 Subcellular Localization of RGH3 Protein Isofo rms ................................ .......... 27 Discussion ................................ ................................ ................................ .............. 28 Materials and Methods ................................ ................................ ............................ 33 Cloning and Sequencing of Rgh3 ................................ ................................ ..... 33 Western Blot Analysis of RGH3 Proteins ................................ .......................... 34 Subcellular Localization Studies ................................ ................................ ....... 35 3 RGH3 FUNCTION IN THE SPLICEOSOME ................................ ........................... 42 Introduction ................................ ................................ ................................ ............. 42 Results ................................ ................................ ................................ .................... 44 RGH3 UHM Domain is Structurally Fit for Protein Protein Interaction .............. 44 RGH3 Co localizes with U2AF 65 a at Sites of Transcription .............................. 45 RGH3 Natural Protein Isoforms Fail to Co localize with U2AF 65 ...................... 47 RGH3 Interacts with U2AF 65 a in planta ................................ .......................... 47 Discussion ................................ ................................ ................................ .............. 48 Materials and Methods ................................ ................................ ............................ 51 Protein Se quence Alignment ................................ ................................ ............ 51


6 Subcellular Localization Studies ................................ ................................ ....... 52 4 ANALYSIS OF THE rgh3 umu1 HYPOMORPHIC ALLELE ................................ .... 58 Introduction ................................ ................................ ................................ ............. 58 Results ................................ ................................ ................................ .................... 61 Mu transposon Insertion Produces a r gh3 umu1 Hypomorphic Allele .............. 61 RGH3 umu is Found in vivo and Shows Partial Co localization With U2AF 65 ... 62 Rgh3 is Required For a Subset of RNA Splicing Events ................................ .. 64 Discussion ................................ ................................ ................................ .............. 65 Materials and Methods ................................ ................................ ............................ 69 In vitro Transcription/Translation and Western Blot Analysis of RGH3 Proteins ................................ ................................ ................................ ......... 69 Subcellular Localization Studies ................................ ................................ ....... 69 RT PCR Analyses of Alternatively Spliced Maize Gen es ................................ 69 5 MAPPING OF THE rgh3 umu1 SEEDLING GENETIC MODIFIER AND THE dek*9700 LOCUS ................................ ................................ ................................ ... 75 Introduction ................................ ................................ ................................ ............. 75 Results ................................ ................................ ................................ .................... 77 A Dominant rgh3 Seedling Modifier is Present in the B73 Maize Inbred .......... 77 Development of a Distributed SSR Marker Set ................................ ................ 78 Mapping of rgh3 Seedling Genetic Modifier ................................ ...................... 80 Mapping of dek*9700 from UniformMu Population ................................ ........... 81 Discussion ................................ ................................ ................................ .............. 82 Materials and Methods ................................ ................................ ............................ 86 Plant Material ................................ ................................ ................................ ... 86 SSR Testing and Scoring ................................ ................................ ................. 87 6 CONCLUSIONS ................................ ................................ ................................ ..... 97 Regulation of RGH3 ................................ ................................ ................................ 97 RGH3 Splicing and Post Splicing Activities ................................ ............................ 98 rgh3 umu1 Allele Reveals Developmental Roles for RGH3 ................................ .... 99 LIST OF REFERENCES ................................ ................................ ............................. 101 BIOGRAPHICAL SKETCH ................................ ................................ .......................... 112


7 LIST OF TABLES Table page 2 1 Number and classes of Rgh3 alternative spliced variants ................................ .. 41 4 1 Maize genes surveyed for splicing defects in rgh3 umu1 mutants ..................... 74 5 1 Modified vs. unmodified scoring of BC1 rgh3/rgh3 seedlings ............................. 95 5 2 Number of co dominant markers identified for each inbred pair from 505 SSR markers ................................ ................................ ................................ .............. 96


8 LIST OF FIGURES Figure page 2 1 RGH3 is homologous to the human URP and its me ssage is alternatively spliced. ................................ ................................ ................................ .............. 37 2 2 Alternative spliced Rgh3 variants produce truncated proteins. ........................... 38 2 3 Western blot analysis of in vitro produced RGH3 protein isoforms.. ................... 39 2 4 Transient expression of GFP tagged RGH3 variants in N. benthamiana ........... 40 3 1 Multiple sequence alignm ent of the conserved ZN UHM ZN region of U2AF35 and URP ................................ ................................ .............................. 54 3 2 RGH3 co localization with U2AF 65 a. ................................ ................................ 55 3 3 RGH3 truncated protein variants fail to co localize with U2AF 65 a.. ..................... 56 3 4 RGH3 interacts with U2AF 65 a in planta. ................................ ........................... 57 4 1 Multiple sequence alignment of RGH3 protein isoforms and rgh3 umu1 mutant allele.. ................................ ................................ ................................ ..... 70 4 2 rgh3 umu1 allele produces a full l ength protein similar to RGH3 protein .......... 71 4 3 RGH3 umu is recruited to speckles and partially co localizes with U2AF 65 a.. .... 72 4 4 RNA splicing defects in rgh3 detected with semi quantitative RT PCR ............ 73 5 1 Abnormal rgh3 seedling phenotype on multiple maize genetic backgrounds. .... 89 5 2 Gradient of abnormal rgh3 seedling phenotype ................................ ................ 90 5 3 Screen for polymorphic SS R markers in B73, Mo17, and W22 ......................... 91 5 4 Genetic map of the distributed marker sets ................................ ....................... 92 5 5 Mapping of the rgh3 umu1 seeding genetic modifier.. ................................ ........ 93 5 6 Fine map of the UniformMu dek *9700 locus.. ................................ ..................... 94


9 LIST OF ABBREVIATION S BP Bra n ch Point BSA Bulk Segregant Analysis DAP Days After Pollination EJC Exon Junction Complex HN RNP HETEROGENEO U S NUCLEAR Ribonucleoprotein Particle NMD Non sense Mediated Decay Py tract Polypyrimidine tract RBD RNA B inding Domain RRM RNA R ecognition Motif RUST Regulated Unproductive Splicing and Translation RGH Rough Endosperm SF1 BBP Splicing Factor 1 Branchpoint Binding Protein SNP Single Nucleotide Polymorphism SN RNP S MALL N UCLEAR Ribonucleoprotein Particle SRSF 1 Serine Arginine rich Splicing Factor 1 SR Serine/Arginine rich SS Splice Site SSR Simple Sequence Repeat TE Transposable Element UHM U2AF 35 Homology Motif URP U2AF 35 Related Protein U2AF U2 Auxiliary Factor ZRSR2 Z inc finger RNA binding motif, Serine A rginine rich 2


10 Abstract of Dissertation Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy STRUCTURE FUNC TION ANALYSIS OF THE RGH3 SPLICING FACTOR IN MAIZE By Federico Martin August 2012 Chair: A Mark Settles Major: Plant Molecular and Cellular Biology Alternative RNA splicing produces multiple mRNA species from individual genes increasing protein divers ity and regulating gene expression. Genome sequencing projects have shown that about 42% to 45% of intron containing genes in plants are alternatively spliced, but little is known about how alternative splicing is controlled. The rough endosperm3 ( rgh3 ) mu tant causes developmental defects that are either seed or seedling lethal. Rgh3 encodes a U2AF 35 related protein ( URP), which is a predicted RNA splicing factor. U2AF 35 proteins identify splice acceptor sites during RNA processing and function through protein protein interactions by creating complexes with U2AF 65 and other Serine/Arginine rich proteins (SR proteins) Semi quantitative RT PCR analyses of alternatively spl iced genes showed that rgh3 affects splicing in a subset of genes supporting a role for RGH3 in alternative splicing. Rgh3 is alternatively spliced, producing at least 19 different spliced variants. Interestingly, only one variant is predicted to encode a full length URP ortholog containing an N terminal acidic domain followed by two zinc fingers (Zn) flanking a U2AF homology motif ( UHM ) domain and a C terminal RS like domain. Several Rgh3 splice variants produce truncated proteins missing one to several do mains. GFP fused to full length RGH3 localized to the


11 nucleolus and nuclear speckles. Functional analysis with the endogenous truncated protein variants and an artificial deletion of the UHM domain fused to GFP showed that while the acidic domain contains a nuclear localization signal, the RS like domain enhances nuclear localization and is also important f or protein recruitment to nuclear speckles. T he UHM domain is a modified RRM domain that allows protein protein interaction and in RGH3 it enables intera ction with U2AF 65 These results suggest that RGH3 participates in the U2 type spliceosome and its function is regulated by alternative splicing creating truncated variants that render the protein unstable and excluded from the splice osome


12 CHAPTER 1 INTRODUCTION The Spliceosome and the Splicing Reaction Eukaryotic genes are made up by coding and non coding regions. Exons generally represent coding regions which are separated by non coding, intervening sequences known as introns. Once genes are transcribed into precursor mRNA (pre mRNA) intron sequences are removed by a mechanism known as RNA splicing (Reddy, 2007). The accurate removal of all intron sequences from pre mRNA is often called constitutive splicing. The splicing reaction takes place co transcriptionally and is catalyzed by a multi protein complex known as the spliceosome. Two types of spliceosome have been identified: a major spliceosome (U2 type), and a less abundant minor spliceosome (U12 type) (Chen and Manley, 2009). While the major spliceosome is found across all eukaryotic organisms, the minor spliceosome is only found in a reduced group including plants and most metazoans, but not i n simple eukaryotic organisms (Patel and Steitz, 2003). The spliceosome is a very dynamic complex assembled in a multistep process that involves RNA RNA, RNA protein and protein protein interactions many of which require ATP hydrolysis. Each step of splice osome assembly requires formation of protein complexes that recognize exon and intron signals to define splicing sites. Splicing is completed after two trans esterification reactions join concomitant exon sequences (Moore and Sharp, 1993). Signals within t he intron include two consensus seq determine splici ng boundaries. A polypyrimidine tract ( Py tract ) the intron to identify the branch point, whi ch is located between 17 40 nucleotides


13 upstream the acceptor site (Reddy, 2001). The first trans esterification reaction takes ite of the intron to form a loop RNA trans esterification reaction (Patel and Steitz, 2003). The accurate recognition of splicing signals and catalysis of the splicing reactions requires the participation of 5 small nuclear ribonucleoprotein particles (snRNPs) and over 150 other non snRNP proteins (Wahl et al., 2009). The major U2 type spli ceosome includes U1, U2, U4, and U6 snRNPs while the minor U12 spliceosome includes the functionally analogous but not identical U11, U12, U4atac, and U6atac snRNPs (Reddy 2007). The fifth snRNP is U5 and functions in both major and minor spliceosomes. In metazoans, the basic processes of spliceosome assembly and catalysis of the splicing reaction are well documented (reviewed in Wahl et al., 2009). Unfortunately, the lack of an in vitro splicing assay in plants has hindered similar biochemical studies in p lant systems. Despite differences in intron composition between animals and plants, plants contain homologs of many of animal proteins involved in spliceosome assembly, including the main snRNPs from the major and the minor spliceosome (Wang and Brendel, 2 004; Lorkovic et al., 2005), arguing for a conservation of the splicing mechanism. The first step of the major spliceosome assembly involves the base pairing of the of the splicing factor 1 (SF1 BBP) to the branch point. This is followed by recognition of


14 complex which also interacts with SF1 BPP. These initial interactions are kn own as the E (early) complex. After formation of the E complex, the U2 snRNP is recruited and base pairs to the branch point in an ATP dependant manner. This process replaces the SF1 BBP to form the pre spliceosome complex A (Chen and Manley, 2009). Next, a pre assembled tri snRNP complex formed by U4/U6 U5 which leads to the formation of the inactivated complex B. In order to become activated, complex B undergoes major conformational and compositional rearrangements that destabilize or release U1 and U4 sn RNPs. The activated complex then undergoes the first catalytic step of splicing forming the lariat intron, a step that generates complex C. Complex C undergoes additional reorganization prior to catalyzing the second reaction to join the exon sequences. Th e final step involves disassembly of the splicing factors and release of the mRNA in the form of messenger ribonucleoprotein (mRNP, Wahl et al., 2009). The minor U12 type spliceosome catalyzes the splicing of a rare class of introns that are diverged from U2 type introns. U12 introns have a longer and more tightly tract. U12 type of introns generally represent less than 1% of the introns in an organism; in Arabidopsis this num ber is about 0.7% (Reddy, 2007). Genes with U12 introns almost always contain other introns of the U2 type (Patel and Steitz, 2003). Despite the intron sequence differences, the assembly steps and conformational changes of the minor spliceosome resembles t hat of the major U2 spliceosome with the exception that U11 and U12 (U1 and U2 homologs respectively ) form a pre spliceosomal complex prior to


15 The spliceosome is also is und er tight regulation. Splicing signals within the pre mRNA are not sufficient to effectively guide the assembly of the spliceosome. In fact, some of these signals need to be recognized multiple times by different factors to ensure a precise splicing reactio n. Many of the interactions taking place in the spliceosome are weak and require multiple splicing factors to form stable complexes (Wahl et al., 2009). This is a crucial principle to confer flexibility to recognize the short and variable splicing signals within an intron. In addition to the core splicing signals, multiple cis acting regulatory sequences in both introns and exons can enhance or inhibit the splicing reaction. These sequences are recognized by trans acting splicing factors which regulate the identification of splicing signals and the assembly of spliceosomal complexes (reviewed in Chen and Manley, 2009). The SR family of proteins is the best studied group of regulatory splicing factors in both plants and mammals. This group of proteins compri ses several phylogenetically conserved and structurally related proteins characterized by a domain rich in arginine and serine residues, known as the RS domain, and one or multiple RNA recognition motifs (RRM). Remarkably, SR proteins are involved in a var iety of functions that not only include regulation of the splicing reaction but also post splicing processes such as mRNA nuclear export, nonsense mediated mRNA decay and mRNA translation (reviewed in Long and Caceres, 2009). Alternative Splicing and Gene Regulation In addition to constitutive splicing, genes containing multiple exons and introns can display a diverse pattern of splicing known as alternative splicing. Alternative splicing generates multiple mRNA products from a single pre mRNA sequence. To do this, the


16 skip entire exons, or to retain entire introns (Nilsen and Graveley, 2010). Alternative splicing can produce unstable mRNA to down regulate protein express ion. These transcript isoforms can also produce multiple protein isoforms with defective or divergent functions to enhance the proteome complexity of eukaryotic organisms. Alternative splicing was initially believed to be a random event that resulted as a by product of constitutive splicing. However, transcriptomic analyses have revealed that more than 90% of intron containing human genes undergo some kind of alternative splicing (Wang et al., 2008). Similar studies in Arabidopsis and rice estimated these numbers to be 42% and 48% of intron containing genes, respectively (Filichkin et al., 2010; Lu et al., 2010), arguing that alternative splicing is widespread. The functional and biological significance of alternative splicing is difficult to prove and a matter of intense investigation. Nevertheless, a variety of studies particularly in metazoans, have demonstrated the relevance of alternative splicing in multiple developmental processes (Black, 2003). Alternative splicing can regulate transcripts by intro ducing premature stop codons (PTC) (Filichkin et al., 2010). Most PTC containing transcripts are targeted for degradation by a quality control survey mechanism known as nonsense mediated decay (NMD). Even though the regulatory bases of this mechanism are n ot yet fully understood, recent studies have suggested that coupling of alternative splicing and NMD likely influences the abundance of functional transcripts, and hence protein levels (Lewis et al, 2003; McGlincy and Smith 2008). The coupling of these mRN A regulatory mechanisms is often called regulated unproductive splicing and translation (RUST) (Lareau et al. 2007a). In metazoans, this is exemplified by the alternative splicing of the


17 Sex lethal ( Sxl ) and transformer ( tra ) genes in D. melanogaster where in each gene, sex specific splicing produces a functional protein product in females. In males, the alternative splicing leads to the inclusion of stop codons, so that no functional protein is produced (Matlin et al., 2005). Similarly, in Arabidopsi s autoregulation by alternative splicing of FCA limits the amount of functional FCA protein to control the transition from vegetative to floral development (Reddy, 2007). The regulatory effects of alternative splicing can also take place post translationa ly. Alternatively spliced transcripts may code for protein isoforms with divergent functions via alternative sub cellular localization or as a protein missing functional domains. For example, it was recently demonstrated that the alternative splicing of th e Arabidopsis SR protein SR45 creates two isoforms with spatially different functions. While SR45.1 plays a major role in flower petal development, SR45.2 is relevant for proper root growth (Zhang and Mount, 2009). Similarly, alternative splicing of SR pro teins may lead to isoforms missing the C terminal RS domain which is relevant for regulation of protein localization and function by phosphorylation (Long and Caceres, 2009). Moreover, studies with SR proteins in Arabidopsis demonstrated that absence of th e RS domain alters sub nuclear localization of proteins likely affecting their function (Tillemans et al., 2005, 2006). Taken together, these examples further highlight the relevance of alternative splicing as a post transcriptional and post translational regulatory mechanism. The U2AF Splicing Complex during formation of the pre spliceosomal complex E (Wahl et al., 2009). The U2AF complex is formed by a large subunit, U2AF 65 and a small subunit, U2AF 35 Both


18 subunits have been identified in most metazoans and plant species based on domain structure and homology (Domon et al., 1998; Wang and Brendel, 2004, 2006a). Each subunit identifies different splicing signals, but cooperative site of the intron and facilitate the recruitment of additional splicing factors. On the one hand, the large U2AF 65 subunit binds the pre mRNA at the Py tract with the help of two of its three RRM domains. (Zamore et al 1992; Mollet et al. 2006). On the other hand, the U2AF 35 of introns, additional factors are nece ssary for their recruitment to true splicing sites. Recently, Tavanez et al. (2012) demonstrated that the heterogenous nuclear ribonucleoprotein A1 (hnRNP A1) proof reads the pre mRNA identifying pyrimidine rich es and facilitates recruitment of the U2AF 35 subunit is believed to be guided by SR proteins bound to exonic splicing enhancer signals (ESS, Long and Caceres, 2009). The binding bet ween both U2AF 65 and U2AF 35 subunits confers stability and the multiple rearrangements of the spliceosome. This binding is enabled by two reciprocal tryptophan (Trp) r in (Kielkopf et al., 2001). In the U2AF 65 subunit, the Trp is found at an N terminal polyproline region between the RS domain and the first RRM domain. Conversely, in the U2AF 35 the Trp residue is located in an RRM like domain known as U2AF homology motif (UHM; Kielkopf et al., 2001, 2004). U2AF 65 also contains a UHM domain located


19 at the C terminal end of the protein. However, this UHM domain does not interact with U2AF 65 Instead, it binds the SF1 BPP sp licing factor and is believed to enhance subsequent recruitment of the U2 snRNP (Selenko et al., 2003; Mollet et al., 2006). The many proteins associated with the splicing reaction provide the necessary flexibility that allows the spliceosome to better react to changes in cell state or the environment. Moreover, it enables the spliceosome to be prepared for the splicing of a wide variety of pre mRNA introns present in an organism and which may require participation of alternative spliceosome components ( Wahl et al., 2009). Even though the U2AF complex is involve in the splicing of the great majority of eukaryotic introns, A recently characterized protein in vertebra tes, known as PUF60, shows high homology to U2AF 65 and was able to substitute U2AF 65 al., 2007).Unlike U2AF 65 CAPER and CAPER are another set of U2AF 65 related proteins (Dowhan et al., 2005). The U2AF 35 Related P rotein (URP) Genome sequence analyses and expression studies have revealed multiple genes encoding protein with similar domain organization and significant homology to the U2AF 35 protein in verte brates. These proteins include U2AF 26 and two highly similar proteins named U2AF RS1 and U2AF RS2 (Tronchere et al, 1997; Shen et at., 2010). The human U2AF RS2, also known as ZRSR2 or U2AF 35 related protein (URP), shows an identical domain distribution as U2AF 35 containing a central UHM domain flanked by two Zn fingers and an RS domain at the C terminal. In addition, URP is characterized


20 by the presence of an acidic domain at its N terminus. This protein was found to be necessary for proper splicing of U2 type introns as demonstrated by splicing analyzes with URP depleted nuclear cell extracts (Tronchere et al., 1997). Moreover, URP was able to interact with U2AF 65 in vitro through its UHM domain.Despite the structural and binding similarities between U2AF 3 5 and URP, their functions do not overlap. Recently, Shen at al. (2010) showed URP participates in splicing of U2 type introns and require during the second catalytic st ep of the spliceosome. Surprisingly, the authors also found URP to participate in splicing of the rare U12 type introns where it also by pull down analyses (Will et al., 20 04). Recently, a homolog of the human URP was identified is maize by Fouquet et al. (2011). The protein, known as ROUGH ENDOSPERM3 (RGH3), was found to be involved in seed and seedling development and is particularly required for proper cell differentiati on at the basal endosperm transfer cell layer (BETL) and embryo surrounding region (ESR). In this work, I analyze Rgh3 transcript processing by alternative splicing and demonstrate that this post transcriptional regulatory system is likely to control the a bundance of functional protein as well as its participation in the spliceosome. Furthermore, I show that RGH3 is able to interact with the U2AF 65 splicing factor and is involved in regulation of a reduce set of alternative splicing events. Overall, the dat a presented here strongly argues that RGH3 has an analogous function to the human URP in maize.


21 CHAPTER 2 ALTERNATIVE SPLICING PRODUCES RGH3 PROTEI N ISOFORMS WITH DIFFERENT FUNCTIONS Introduction Once genes are transcribed into precursor mRNA, intron seq uences are removed by the mechanism of RNA splicing. Alternative splicing can generate multiple mRNA products from a single pre mRNA sequence. The different transcripts from a single gene can either be unstable mRNA or code for protein isoforms with diverg ent functions. Alternative splicing, then, constitutes a versatile form of genetic regulation to influence protein abundance or function. Splicing is catalyzed by a multi protein complex know as the spliceosome. The spliceosome requires the dynamic interac tion of 5 small ribonucleoprotein particles (snRNPs) and over 170 other proteins (Wahl et al., 2009). Two types of spliceosome exist in both plants and animals: a major spliceosome (U2 type), and a minor spliceosome (U12 type). Despite the large number of proteins involved in this process, many of them share common structural domains and are regulated in a similar fashion.One common form of regulation is alternative splicing of these factors. In plants, for example, in silico analysis using Arabidopsis EST and cDNA sequences showed a high frequency of alternative splicing events among splicing related genes (Wang and Brendel, 2004). Further support for this mechanism was drawn from analyses of a well studied group of splicing factors, known as SR proteins, d emonstrating that in both mammals and plants these proteins undergo high levels of alternative splicing (Lareau et al., 2007b; Palusa et al., 2007). SR proteins are a conserved family of proteins that play crucial roles as regulators of constitutive and al ternative splicing by identifying enhancers or repressor sequences, as well as recruiting splicing factors and guiding


22 spliceosome assembly (Isshiki et al., 2006; Shen and Green, 2006). Interestingly, in A rabidopsis splicing of SR proteins is regulated in a developmental and tissue specific manner, and is influenced by hormones and multiple abiotic stresses indicating a true functional control mechanism rather than noise created by the splicing process (Palusa et al., 2007; Ali and Reddy, 2008b). Even tho ugh the regulatory bases of this mechanism are not yet fully understood, recent studies have suggested that coupling of alternative splicing and nonsense mediated decay (NMD) likely influences the abundance of functional transcripts through a mechanism kno wn as regulated unproductive splicing and translation (RUST) (Lewis et al, 2003; Lareau et al. 2007a; McGlincy and Smith 2008). In plants, strong indications for this type of coupling have been demonstrated for SR proteins as well as for several polypyrimi dine track binding proteins (Palusa and Reddy, 2010; Stauffer, 2010). In mammals, as in plants, members of the pre mRNA splicing machinery typically show a punctuated distribution throughout the nucleoplasm while recruited into sub nuclear structures such as the nucleolus, cajal bodies, and speckles (Lamond and Spector, 2003; Tillemans et al., 2005; Shav Tal et al., 2005; Lorkovic et al., 2008; Koroleva et al., 2009; Stauffer et al., 2010). The nucleolus is the most prominent sub nuclear compartment, though very few splicing factors were found to exclusively localize to this compartment (Pendle et al., 2005). However, multiple factors, especially snRNPs, have been shown to transiently pass through it as part of their maturation process (Lorkovic et al., 2004 ; Ali and Reddy, 2008a). Interestingly, several factors that do not localize to the nucleolus under normal conditions were seen to re localize into it as a product of different stresses (Tillemans et al., 2005, 2006). Nuclear speckles are


23 located in the in terchromatin space in the nucleoplasm, and are one of the major splicing factors storage sites (Spector and Lamnod, 2011). Mostly known for recruiting SR proteins, nuclear speckles also house snRNPs and non snRNPs as well as additional RNA processing prote ins. In addition, they have been observed near active transcription sites and recently pre mRNA have been detected in areas immediately adjacent to nuclear speckles indicating that these structures serve as storage and assembly areas for RNA processing fac tors (Reddy et al., 2012). Importantly, nuclear speckles are dynamic structures which formation and size are influenced by multiple processes including cell cycle, cell type and transcriptional activity (Spector and Lamnod, 2011; Ali and Reddy, 2008a and r ef. therein). Here, I describe the maize RGH3 protein, a SR like protein that shows high degree of homology to the human U2AF 35 Related Protein (HsURP), also known as ZRSR2. HsURP was first characterized by Tronchere et al. (1997) as an alternative splicin g factor that participates in the U2 spliceosome. It was later demonstrated that HsURP also interacts with U12 spliceosome complex members and participates in splicing of rare U12 introns (Will et al., 2004; Shen et al., 2010). Through structural and funct ional analysis of Rgh3 transcripts and RGH3 protein isoforms, I demonstrate that alternative splicing of Rgh3 affects protein localization, likely regulating protein function. Results The Rgh3 Transcript is Alternative Spliced Rgh3 was originally identified by Fajardo (2008) while screening for seed mutants affecting endosperm embryo interactions in maize. The Rgh3 locus is not correctly assembled in the current B73 AGPv2 reference genome ( To sequence and ass emble the locus, I cloned the genomic locus as two overlapping


24 fragments from the maize BAC ZMMBBc497J22. Once cloned, the fragments were sequenced by primer walking and assembled into a single contig. To identify the Rgh3 exons, I designed primers spannin g the entire predicted coding region and tested seedling cDNA by RT PCR. Numerous products were amplified andcloned, and from these 45 independent RT PCR products were sequenced. These represented 19 Rgh3 splice variants with the potential to encode seven protein variants (Genbank Accessions: JN791417 to JN791436). Rgh3 transcript isoforms result from variable 1A shows schematics forrepresentative Rgh3 mRNA isoforms that code for the seven protein isoforms. The Rgh3 isoform contains the full length coding sequence and is composed of 10 exons and retention of intron 1. The sequence encodes a predicted 755 amino acid peptides and shares significant protein sequence identity with HsURP at the central region composed of a UHM domain (Kielkopf et al., 2004) flanked by two CCCH type Zn Finger domains. Similar to HsURP, RGH3 contains an N terminal acidic domain, and an arginine/serine rich (RS) region at its C terminus. By contrast, H sU2AF35 is less identical to RGH3 in the central domains and does not contain an acidic N terminal region. For these reasons, I conclude RGH3 is homologous to human U2AF35 Related Protein (URP) (Tronchere et al., 1997). RGH3 shows considerable sequence ide ntity and domain structure with a likely ortholog in Arabidopsis (Figure 2 1B). The 18 other Rgh3 isoforms identified in this study have a range of coding potential. Splicing of intron 1 produces a likely noncoding message; nevertheless it retains an unin terrupted URP reading frame that could initiate translation at a downstream start codon found within the UHM domain. Similar to Rgh3 Rgh3


25 isoforms skip exon 6 and 7 but shows alternative splicing at exon 10 that creates a frame shift and premature termi nation codon (PTC) at the second zinc finger. Rgh3 also excludes exons six and seven but retains intron three. Retention of intron three causes a frame shift that incorporates a PTC and produces a truncated protein containing the N terminal acidic domain exclusively. Isoforms Rgh3 Rgh3 Rgh3 and Rgh3 have variations involving exons five, six, seven, and/or introns five, six and seven. These splicing events create frame shifts in the coding sequence introducing several new amino acids but ultimately p roducing a PTC either at the first zinc finger or the UHM domain (Figure 2 2A). Among the 19 identified splice variants, many include are technically different splic e variants even though they code for one of the seven protein isoforms. For example, 4 different classes of transcripts were found to retain exon 6 but also included additional splicing events downstream. Exon 6 retention results in a transcript that codes for RGH3 and a total of 11 of the 45 sequenced cDNA clones belonged to one of these 4 classes (Figure 2 2A, Table 1 1) Protein Coding Potential of Rgh3 Transcript Isoforms The alternatively spliced Rgh3 isoforms have the potential to regulate RGH3 protein expression either by destabilizing Rgh3 transcripts or by altering RGH3 protein domains (Zang and Mount, 2009; Stauffer et al., 2010). To determine whether Rgh3 variants code for proteins in vivo I des igned peptide antibodies (Ab) targeting the N and C terminus of the RGH3 protein. I then tested the Ab on protein extracts from multiple normal tissues of several maize inbred backgrounds (Figure 2 2). The RGH3 protein is predicted to be 86 kDa (Figure 2 2A). As observed in Figure 2 2B, western


26 blot analyses show mixed results. The N terminal Ab seems not to detect any proteins in either seedling or root tissues. On the contrary, it detects multiple bands in 24 days after pollination (DAP) seed protein e xtracts. None of these bands match the predicted sizes for RGH3 protein isoforms. The C terminal Ab, detected a band of 125 kDa only in seedlings tissues, and a single band of 56 kDa in seed tissue. In order to reconcile these results and to experimental ly determine the SDS PAGE electromobility of the RGH3 protein isoforms, I cloned Rgh3 Rgh3 Rgh3 and Rgh3 cDNA and tested them in in vitro transcription/translation reactions using wheat germ extracts (Figure 2 3). The Rgh3 variant was not included because the N terminal peptide antibody epitope lies just downstream of the PTC created in the variant (see Materials and Methods for information regarding Ab). Both, the N and C terminal Ab confirmed that RGH3 protein is 125 kDa. These data suggest the proteins detected in western blots using in vivo protein extracts represent RGH3 The three alternatively spliced variants produced translation products that cross reacted with the N terminal anti RGH3 antibody, but not wit h the C terminal antibody (Figure 3). As observed for RGH3 the detected proteins are slightly larger than the expected 42, 33.5 and 30 kDa molecular weight for RGH3 RGH3 and RGH3 isoforms respectively. The results suggest that alternatively spliced Rgh3 isoforms are capable of producing truncated protein versions of RGH3 and are likely to be found in vivo Due to technical difficulties involving protein extraction and blotting, I have not been able to further confirm these results.


27 Subcellular Locali zation of RGH3 Protein Isoforms To study the sub cellular localization and distribution of RGH3 protein isoforms, I created green fluorescent protein (GFP) N terminal fusions with RGH3 RGH3 RGH3 RGH3 and RGH3 Each construct was transiently expressed in N. benthamiana leaves using Agrobacterium mediated infiltration. In these experiments, RGH3 localized to the nucleolus at all times and was frequently found in nuclear speckles (Figure2 4). Since RGH3 is the predicted full length protein, it is likely that its localization reveals structures where the protein is functional. It is also possible that transient over expression may reveal locations where the protein is sequestered if it accumulates to excessively high levels. The RGH3 RGH3 RGH3 and RGH3 isoforms localized only to the nucleolus and faintly disperse in the nucleoplasm (Figure 2 4). Interestingly, all tested truncated protein variants also localized in the cytoplasm. Under similar conditions o f laser intensity and gain at the fluorescent microscope, the fluorescent signal emitted by these protein fusions was much lower compared to that emitted by GFP RGH3 The difference in signal could be attributed to a lower stability of the truncated mRNA which translate into lower protein abundance, or to the stability of the protein variants themselves. Together, these data suggest that RGH3 localization results from interacting signals within the acidic, and RS domains. On one hand, the acidic domain con tains a nuclear localization signal, while on the other the RS domain appears to be important for recruitment of the RGH3 protein into nuclear speckles, a phenomenon already observed with other RS domain containing proteins (Tillemans et al., 2005). In


28 add ition, localization of the truncated protein variants to both the nucleus and cytoplasm indicates that the RS domain also influences nuclear localization. The dynamic localization shown by the truncated variants seems not to be influenced by the presence o r absence of the UHM domain. To test this hypothesis, I created a UHM domain deletion transcript and fusedit to GFP. As observed in Figure 2 4B, the fusion protein localizes to the nucleus. Like the full length RGH3 the protein is also found in the nucle olus but it localized to nuclear speckles much more often and readily than the full length protein. The localization of this construct demonstrated that the acidic domain is necessary for nuclear localization, though it is not sufficient for this task as t he RS domain seems to aid proper nuclear and sub nuclear localization. Also, the experiment confirms the importance of the RS domain for nuclear speckle recruitment. UHM domains have the ability to act as protein protein and/or protein RNA binding domains (Kielkopf et al., 2004). It is therefore feasible that the RGH3 UHM domain facilitates localization to the nucleolus by enhancing interaction with other factors within this sub nuclear compartment. Absence of the UHM domain may have weakened RGH3 ability t o target other proteins or mRNAs in the nucleolus and thus enhance RS domain capacity to recruit the protein into speckles. Discussion All higher eukaryote genes containing intronic regions must undergo splicing of their pre mRNA in order to produce a mature mRNA ready for translation. Through alternative splicing, a single pre mRNA with multiple introns can give rise to various mRNAs whi ch can generate either unstable mRNA or code for different protein isoforms with defective or divergent functions (Reddy, 2007). Originally considered to be a


29 random phenomenon, alternative splicing is increasingly gaining attention as a versatile form of post transcriptional regulation with vast implications for the transcriptome and proteome of eukaryotic organisms. In plants, recent studies in Arabidopsis and rice estimated that 42% and 48% of intron containing genes, respectively, undergo some type of alternative splicing (Filichkin et al., 2010; Lu et al., 2010). In humans, this number increases to over 90% of the transcripts (Wang et al., 2008) indicating that this is a widespread mechanism rather than a by product of constitutive splicing. The compl ete biological consequences of alternative splicing are difficult to realize. Nevertheless, the involvement of this mechanism in relevant developmental processes is well established and characterized. One of the best understood developmental pathways conce rning alternative splicing is the sex determination pathway in Drosophila (reviewed in Matlin et al., 2005) In plants, the role of alternative splicing as a regulatory system is as not as defined as in metazoans. However, several investigations have demon strated its effects in multiple developmental and defense response pathways. For example, the alternative splicing of FCA pre mRNA acts as a developmental switch between vegetative and reproductive phases in Arabidopsis (Quesada et al., 2003; reviewed in L orkovic, 2009). Regulation of splicing factors by alternative splicing provides conclusive evidence in splicing, the SR family of splicing factors is the best studied g roup in metazoans as well as in plants. In humans, 11 SR proteins have been identified compared to 18 found in Arabidopsis and 24 in rice (Barta et al., 2008). Plant and mammalian SR proteins undergo high levels of alternative splicing, and many of the spl icing events are


30 conserved across species (Iida and Go, 2006; Lareau et al., 2007a; Palusa et al., 2007). In fact, SR proteins in both mouse and humans were shown to undergo the same alternative splicing patterns which take place at ultra conserved element s within their sequences (Lareau et al., 2007a). In plants, how alternative splicing is regulated and the actual function of alternative spliced variants is not well understood, however, many of alternative spliced variants were found to include pre termin ation codon (PTC) (Palusa et al., 2007; Tanabe et al., 2007; Filichkin et al., 2010). Most PTC containing transcripts are targeted for degradation by nonsense mediated decay (NMD), a common RNA surveillance mechanism found in most eukaryotes (Chang et al., 2007; Muhlemann et al, 2008). If left unprocessed, translation of PTC containing transcripts could produce truncated proteins, as is the case for RGH3 isoforms (Figure 2 2), with potential negative effects for the cell. Based on multiple studies showing e xtensive coupling between alternative splicing and NMD, it was suggested that alternatively spliced variants containing PTCs may regulate the abundance of functional transcripts through the RUST mechanism (reviewed in Lareau et al., 2007b). Consistent with this hypothesis, extensive coupling between NMD and the abundance of alternative spliced variants of SR proteins and other important genes was recently observed in Arabidopsis (Palusa and Reddy, 2010; Kalyna et al., 2012). Here, I demonstrate that the Rgh 3 transcript undergoes high levels of alternative splicing, producing spliced variants containing PTC (Figure 2 1B). The observed frequency of Rgh3 spliced variants could be explained by the RUST mechanism. However, the high frequency of Rgh3 cDNA clones containing a PTC suggests that the PTC transcripts are either stable and translated or they are produced at very high frequency when compared to the full length


31 mRNA. Additional experiments are required to determine whether Rgh3 transcri pts are subject to RUST regulation. Overall, this example further demonstrates the importance of alternative splicing as a mean of post transcriptional control. Alternative splicing can also have post translational repercussions by creating protein isoform s with alternative functions or sub cellular localization. Once again, regulation of SR proteins provides a clear example for this mechanism. SR proteins have a modular structure, typically containing one or two copies of an RRM (RNA recognition motif) dom ain at the N terminus and a C terminal RS domain. RRM domains provide RNA binding specificity and RS domains promote protein protein interactions that facilitate recruitment of the spliceosome. In addition, RS domains tend to act as a nuclear localization signals (NLS) affecting the subcellular localization of SR proteins by mediating the interaction with the SR protein nuclear import receptor, transportin SR (Long and Caceres, 2009). RS domains are highly phosphorylated, offering an additional level of con trol for the activity of SR proteins. For example, in mammals, phosphorylation state of the RS domain of the serine arginine rich splicing factor 1 (SRSF1) is known to control sub cellular localization of the protein and to modulate interaction with the U1 70k unit of the U1 snRNP to initiate spliceosome assembly (Cho et al., 2011). Based on these examples, the RS domain of RGH3 may also be required for localization of the protein into the nucleus indicating that even though the NLS is found in the acidic d omains, this domain may not be sufficient for nuclear localization. Moreover, since the RS domain of SR proteins is located at the C terminal end, alternative splicing of these proteins is likely to produce truncated protein isoforms missing the RS domain. This, in turn, not only would prevent protein regulation


32 by phosphorylation but also affect sub cellular localization and recruitment to the spliceosome. For example, deletion of the RS domain of the Arabidopsis SR protein RSZp22 influenced re distributio n of the protein from nuclear speckles to the nucleolus (Tillemans et al., 2006). Consistent with these observations, RGH3 isoforms lacking the RS domain fail to localize into speckles suggesting the RS domain is needed for their recruitment into speckles. In addition, the presented data argues that RGH3 truncated protein variants are likely to be non functional due to the alternative sub cellular localization and failure to be recruited to spliceosomal speckles. Finally, the full length RGH3 protein was f ound to be localized in the nucleolus (Figure 2 3). The nucleolus is not a common storage site of splicing factors under normal conditions. RNA splicing factors typically accumulate in nuclear speckles and/or cajal bodies (Reddy et al., 2012). Different st ress conditions including hypoxia, heat shock, phosphorylation state or inhibition of transcription can cause some splicing factors to move into the nucleolus in plants (Tillemans et al., 2005, 2006; Koroleva et al., 2009). Based on these prior observation s, the transient expression of RGH3 isoforms may cause cellular stress leading to localization to the nucleolus. Historically, the nucleolus has been known as the site of ribosomal RNA transcription and processing. Moreover, it has been linked to processin g and assembly of a variety of RNPs, control of cell cycle and senescence, and as a sensor of stress (Brown and Shaw, 2008). Data from recent studies, however, has implicated the nucleolus in a wider range of functions including transcriptional gene silenc ing, and mRNA export and surveillance (Pendle et al. 2005; Brown and Shaw, 2008). Additionally, a higher abundance of aberrantly spliced mRNA were found in plant nucleolus compared to the


33 nucleoplasm suggesting that the processing of aberrant mRNAs may tak e place in this compartment (Kim et al., 2009). Interestingly, many splicing factors, particularly SR family members, have been implicated in post splicing mechanisms including mRNA nuclear export, NMD, and mRNA translation (Long and Caceres, 2009). Based on these observations, RGH3 localization in the nucleolus argues for its potential involvement in pre mRNA splicing as well as post splicing activities that may take place in the nucleolus. In conclusion, I have shown that the Rgh3 splicing factor gene pr oduces numerous splice variants that introduce PTCs in the resulting mRNAs. Based on in vivo and in vitro reactions, and transient GFP fusion expression assays these variants have coding capacity. However, expression of the truncated forms suggests Rgh3 ma y be under RUST regulation in order to modulate the level of functional transcripts. The data indicate that alternative splicing of Rgh3 produces non functional proteins acting as an additional level of regulation of RGH3 RGH3 localizes to nuclear speckl es, consistent with the localization of multiple other splicing factors, and also into the nucleolus. Data from the human homologue and observed nucleolus localization of RGH3 argues for a potential involvement of RGH3 in splicing and post splicing related functions. Combined these data suggest alternative splicing of the RGH3 gene regulates functional transcripts and protein function. Materials and Methods Cloning and S equencing of Rgh 3 The Rgh3 locus was subcloned from the B73 maize BAC ZMMBBc497J22. The BAC was digested with HindIII and the fragments were cloned into pBluescript vector


34 (Thermo Scientific, USA). Rgh3 contains a HindIII restriction site within intro 4 splitting rd southern blot technique using a 535bp probe spanning intron 1, exon 2 and intron 2. Rgh3 locus was amplified in its entirety by PCR using Takara LA high fidelity taq DNA polymerase (New England Biosciences) and cloned into pTOP sequenced by primer walking. Sequenced fragments were then assembled into using Vector NTI s oftware (Invitrogen). Rgh3 spliced variants were amplified from seed cDNA by RT PCR using Phusion RT PCR products were cloned into pTOPO vector (Invitrogen). 45 total clo nes containing insertions over 2 kb were selected and sequenced by Sanger sequencing. W estern B lot A nalysis of RGH3 P roteins Two regions at the N terminus (SAQEVLDKVAQETPNFGTE aa 202 to 220), and C terminus (STKDDKRRKHHSGNRWH, aa 692 to 709) of the RGH3 pr oteins were targeted to produce peptide a ntibodies. Peptides were synthesized, purified and used to raise polyclonal a ntibodies in rabbit (Bio Synthesis, Lewisville, TX). Extraction of total protein was performed as described in Abdalla et al. (2009) with the following modifications: fresh instead of frozen tissue was used for extraction, and a single filtration step was performed instead of two. Total protein extraction was used for western blot analyzes instead of nuclei fraction. For in vitro react ions, Rgh3 variants were sub cloned from pENTR vectors (see below) using the following primers. Primers contain restriction digestion sites for Sgf1


35 (Promega) and Pme1 (New England Bio Labs) enzymes. PCR products were cloned into pF3AWG vectors (Promega, # L5671) through restriction digestion using above mentioned restriction enzymes and ligated using T4 DNA ligase enzyme as per transcription/translation reaction using TnT SP 6 high yield wheat germ protein A total of 10 l of protein extract and 12l of TnT reaction were separated in an 8% gel by SDS PAGE and blotted with anti RGH3 peptide antibodies raised ag ain s t the N terminal acidic domain (1/3000 dilution) and the C terminal RS domain (1/5000 dilution) of RGH3 Subcellular Localization Studies N and C terminal GFP fusion proteins were constructed by cloning cDNAs for RGH3 isoforms into pDONR221 or pENTR vectors (Invitrogen) according to the FWG2 for C terminal GFP fusions or pB7 WGF2 for N terminal GFP fusions (Karimi et al., 2002, 2007) by LR deletion construct, cDNA from Rgh3 terminal stop codon. Both fragments were later lig ated by overlap extension (sewing) PCR (Horton et al., 1989), and the obtained product was cloned into pENTR (Invitrogen) and sequenced. The entire fragment was then cloned into pB7 WGF2 as explained above. Transient expression experiments in Nicotiana ben thamiana were completed essentially as described by Kapila et al. (1996) with the following modifications. Binary


36 vectors were transformed into Agrobacterium tumefaciens strain ABi by a freeze thaw method (Wise et al., 2006). MES was not included in the Ag robacterium growing media, and N. benthamiana infiltration was completed with a 10 mL needleless syringe on 4 to 5 week old plants grown in growth chamber at 22 to 24C with 16/8 h day/ night. For colocalization experiments, Agrobacterium strains carrying individual plasmids were mixed in a 1:1 ratio prior to infiltration. Fusion protein expression was visualized 24 to 48 h after transient transformation, and representative pictures of subcellular localization were obtained using a Zeiss Pascal LSM5 confoca l laser scanning microscope as previously described (Pribat et al., 2010).


37 Figure 2 1. RGH3 is homologous to the human URP and its message is alternatively spliced. A) Schematic of the Rgh3 locus (top panel). Alternative splicing gives rise to at least 19 splice variants, signified by Greek letters. Gray boxes indicate exons required to code the RGH3a protein, and open boxes are skipped exons for this isoform. Thick black lines indicate intr ons that are splice sites. Examples of splicing patterns that code for seven RGH3 protein variants are shown at the bottom. Alternatively splicing event s introduce premature ter mination codons (PTC) indicated by red signs B) Schematic of protein domains of URP and U2AF35 homologs. Sequence identity to the RGH3 Zn UHM Zn region is indicated. Zn, zinc finger. At, Arabidopsis thaliana ; Hs, Homo sapiens.


38 Figure 2 2 Alternative spliced Rgh3 variants produce truncated proteins. A) Schematic of the full length and several truncated RGH3 protein isoforms detailing present and missing domains of each isoform. Peptides conforming each isoform are detailed on the right with additional amino acids introduced by changes in the frame of translation are indicated in parentheses; predicted protein sizes are specified on the left (not drawn to scale). B) Western blot analysis of protein extracts from multiple Rgh3/rgh3 tissues in W22 and B73 maize inbred backgrounds. Proteins were detected with N terminal (left panel) and C terminal (right panel) peptide antibodies (see Material and Methods for antibody information).


39 Figure 2 3. Western blot analysis of in vitro produced RGH3 normal and truncated protein isoforms. Proteins were detected with N terminal (left panel) and C terminal (right panel) peptide antibodies. Detected bands are of similar sizes to those detected in protein extracts from normal tissues indicating that sizes for protein isoforms were underestimated and are present in vivo A non specific band was detected by the N terminal antibody that was also present in the no vector control (arrow).


40 Figure 2 4 Transient express ion of GFP tagged RGH3 variants in N. benthamiana leaves. A) Some of the RGH3 isoforms identified were tagged with GFP to analyze their localization RGH3 loca lized to the nucleolus, to nuclear speckles and diffuse in the nucleoplasm. The remai ning protei n variants localized to nucleolus and remained diffuse in the nucleoplasm but not nuclear speckles. Expanded field of view demonstrate s localization to cytoplasm. B) RGH3 UHM deletion variant localized to the nucleolus and was enriched in nuclear speckles but not in the cytoplasm White scale bar = 5m; red scale bar = 40m.


41 Table 2 1. Number and classes of Rgh3 alternative spliced variants Isoform group No. of transcripts coding for the same isoform Percentage No. of different events producing same isoform* RGH3 1 1 24.4% 1 RGH3 11 24.4% 4 RGH3 1 9 42.2% 8 RGH3 1 2.2% 1 RGH3 1 2.2% 1 RGH3 1 2.2% 1 RGH3 1 2.2% 1 *Isoform groups may include multiple transcripts containing several different splicing events that ultimately give rise to one of the indicated protein isoforms


42 CHAPTER 3 RGH3 FUNCTION IN THE SPLICEOSOME Introduction Splicing of introns by the spliceosome is a dynamic event that takes place co transcriptionally. Proper formation of the spliceosome requires the stepwise assembly of smaller protein complexes that identify intronic as well as exonic signals, and catalyze two trans esterification reactions (Chen and Manley, 2009). In metazoans, it has been splicing signal by the U1 70K snRNP in cooperation with the SR protein SRSF1 (Ch o et spliceosome assembly include identifying the branch point (BP) by SF1 BBP. Subsequently, SF1 BBP interacts with the U2 auxiliary factor (U2AF) complex, which binds t Together, these interactions are known as the spliceosome E (early) complex. The next spliceosome assembly step is the recruitment and binding of the U2 snRNP by the U2AF comple x. This allows U2 snRNP to base pair with the BP in an ATP dependant manner while displacing SF1 BBP to form what is known as complex A (Wahl et al., 2009). The U2AF is a heterodimer complex formed by two sub units, the large U2AF 65 and the smaller U2AF 35 Both subunits are SR like proteins containing an RS domain and RRM domains. U2AF 35 contains a single RRM, while U2AF 65 has three RRM domains (Mollet, 2006). Interestingly, the RRM domain in U2AF 35 and the third RRM domain in U2AF 65 belong to a new class o f RRM domain termed U2AF homology motif (UHM) (Kielkopf et al., 2001; Selenko et al., 2003). UHM domains are able to adopt a


43 typical RRM topology and have the potential to interact with RNA. However, they contain unique features that allow them to bind pro teins as well (Kielkopf et al., 2004). spliceosome functioning. Through its UHM domain U2AF 65 is able to interact with SF1 BPP to enable recognition of the BP (Selenko et al., 2003, Banerjee et al., 2004). Similarly, U2AF 35 binds U2AF 65 through its UHM domain to enhance recognition of the large and small sub units do not interact directly with each other. Instead, the U2AF 35 UHM binds U2AF 65 at an N terminal polyproline region between the RS domain and the in residues (Kielkopf et al., 2001). The Trp of the UHM domain in U2AF 35 is flanked by an arginine (Arg) and a phenyla lanine (Phe) residue, a motif known as Arg X Phe motif (where X is any amino acid), located in a hydrophobic pocket where the interaction takes place. The Arg X Phe motif is one of the key features that distinguish UHM domains from canonical RRM domains (K ielkopf et al., 2004). The human URP, a protein showing similar domain structure and homology as U2AF 35 was found to support splicing of U2 type introns and interacted with U2AF 65 in vitro through its UHM domain (Tronchere et al, 1997). Moreover, URP func tion is non redundant with that of U2AF 35 as U2AF 35 fails to complement URP depleted nuclear extracts for in vitro splicing activity. Interestingly, Shen et al. (2010) revealed that URP is also able to participate in U12 type intron splicing demonstrating that URP can interact with both spliceosomes even though it influences distinct steps of splicing for U2 and U12 introns. The RGH3 protein in maize shows significant conserved homology


44 with human URP at its central region and shares the URP domain structur e suggesting it is likely an ortholog of URP. In this section, I provide evidence suggesting that RGH3 participates in the U2 spliceosome and shows similar protein protein interactions as the human URP. Results RGH3 UHM D omain is Structurally Fit for Prote in P rotein I nteraction The central Zn UHM Zn domain in RGH3 shows significant homology with URP proteins in human and is a bit more distantly related to the same domains in U2AF 35 (Figure 2 1). In plants, neither U2AF 65 /U2AF 35 nor U2AF 65 /URP interactions h ave been studied in detail. To investigate whether the same interactions could occur in plants, I compared the peptide sequences from the Zn UHM Zn domains of U2AF 35 and URP from human, maize, rice, and Arabidopsis (Figure 3 1) The protein sequence alignm ent demonstrates that the hydrophobic pocket of the U2AF 35 protein is poorly conserved between human and plant species, but is highly conserved among plant homologs (Figure 3 1A, red underline). Unlike U2AF 35 the hydrophobic pocket of URP proteins is bett er conserved across species, even though they are not identical (Figure 3 1B, red underline). Comparison of the Arg X Phe motif presents a different scenario. In the UHM domain of both U2AF 35 and URP, the Arg X Phe motif shows higher conservation between h uman and plant samples (Figure 3 1, orange box). Even though the Arg X Phe motif is a signature motif that distinguishes UHM domains from canonical RRM domains, variations at the Phe position for similar bulky aromatic amino acids have been observed in oth er UHM containing proteins (Kielkopf et al., 2004). While the human U2AF 35 protein presents a signature Arg Trp Phe motif (Trp denotes Tryptophan), maize and rice proteins show a conserve Arg Tyr Tyr (Tyr denotes


45 Tyrosine) and Arabidopsis shows an Arg Trp Tyr. Similar residue changes are observed in URP proteins (Figure 3 1B, orange box). The human URP protein contains an Arg Trp Tyr motif while all the plant proteins have a conserved Arg Tyr Phe. It is important to highlight that the above mentioned amino acid changes involve substitutions for similar bulky aromatic amino acids which may not significantly alter the phobicity of the binding pocket. Interestingly, plant homologs of both U2AF 35 and URP contain a Tyr residue instead of a Trp at the X position w in 35 and U2AF 65 This change, however, is consistent with a Trp to Tyr residue exchange observed in plant U2AF 65 proteins at the likely binding site with U2AF 35 These residue changes in evolved to take place among Tyr residues instead of Trp (Kielkopf et al., 2004). Taken together, the data argues that the changes in the UHM domain hydrophobic pocket of plant URP proteins may not significantly alte r the phobicity or conformation of the binding pocket. Furthermore, the residue changes in the Arg X Phe motif of UHM domains is compensated by a similar change in U2AF 65 arguing for a conserved re in place. RGH3 Co localizes w ith U2AF 65 a at Sites of T ranscription If RGH3 interacts with maize U2AF 65 in a similar manner as found in vertebrates, I expect both proteins to localize to overlapping sites within the nucleus. To test this hypothesis, I cloned the maize versions of the U2AF 65 a and U2AF 35 a proteins and fused them to either GFP or RFP. The constructs were expressed either individually or in combination with RGH3 through agrobacterium mediated transient expression in N. benthamiana leaves (Figure 3 2). U2AF 65 a localized to the nucleoplasm and was


46 concentrated into nuclear speckles. Similarly, U2AF 35 a localized to the nucleoplasm and showed concentration to nuclear speckles as previously observed for the Arabidopsis protein (Wang and Brendel, 2006a). In contrast to RGH3, none of the U2AF factors localized to the nucleolus (Figure 3 2A). When RGH3 was co expressed with U2AF 65 a, both proteins showed a similar distribution in the nucleoplasm (Figure 3 2B). Even though n uclear speckles were not clearly defined, both proteins concentrated in similar structures and also showed a similar disperse localization within the nucleoplasm. The co localization was not always observed since at times both proteins localized to differe nt locations in the nucleoplasm (data not shown), possibly due to either the viability of the tissue or cell cycle state of the cell which has been shown to influence re arrangement of nuclear speckles or transcriptional activity of the cell (Fang et al, 2 004; Spector and Lamond, 2011). Interestingly, U2AF 65 a signal was also observed into the nucleolus suggesting a re arrangement of its localization due to the presence of RGH3 (Figure 3 2B, red arrowhead). As a control, I also tested the co expression of U 2AF 65 a and U2AF 35 a tagged with GFP and RFP, respectively (Figure 3 2C). Expression of both proteins showed a similar distribution in the nucleoplasm but not in the nucleolus, indicating a potential conserved interaction between the proteins to form the U2A F heterodimer complex in plants. Once again, nuclear speckles were not clearly defined and the observed co localization was dispersed in the nucleoplasm at likely sites of transcription. Taken together, the data indicate that RGH3 and U2AF 65 have overlapp ing localization in the nucleus and high levels of RGH3 expression seem to influence U2AF 65 sub nuclear localization. These observations support a conserved interaction of the proteins in vertebrates and plants (Tronchere et al, 1997).


47 RGH3 Natural Protei n I soforms Fail to Co localize w ith U2AF 65 In chapter 2, I showed that truncated RGH3 variants express at low levels and do not localize like full length RGH3 (Figure 2 3). Potentially, the missing domains of RGH3 variants could affect colocalization with U2AF 65 a. To analyze this possibility, I co expressed several natural RGH3 truncated variants with U2AF 65 a RFP fusion protein. The tested isoforms include RGH3 which is only missing the RS domain, and RGH3 and RGH3 which contain the acidic domain, the first Zn finger and small a portion of the UHM domain (Figure 2 2B). As shown by the images in figure 3 3, none of the tested variants co localizes with U2AF 65 a. While thesevariants are observed in the nucleolus and partially disperse in the nucleoplasm, U 2AF 65 a remains in the nucleoplasm. Moreover, U2AF 65 a localization is concentrated in nuclear speckles suggesting that truncated RGH3 proteins do not influence U2AF 65 a localization. Taken together, these data argues that the RS and UHM domains are necessary for a potential interaction with U2AF 65 a. RGH3 Interacts w ith U2AF 65 a in p lanta Although co localization data are suggestive of a conserved URP/U2AF 65 interaction in plant cells, this is not direct evidence for protein protein interactions. I used the bimolecular fluorescence complementation (BiFC) assay to address whether the interaction is real and is found in vivo BiFC involves the fusion of two pro teins, one as the bait and the other as a prey, to either the N or C terminal half of a fluorescence protein. If the tested proteins interact, the two halves of the fluorescence protein would come into close proximity, fuse and emit a fluorescent signal u pon excitation (Citovsky et al., 2006). Thus, I fused RGH3 to the N terminal half of the yellow fluorescent


48 protein (YFP) and U2AF 65 a to the C terminal half of YFP. These constructs were transiently co expressed in N. benthamiana leaves. Figure 3 4A shows images from two independent biological tests demonstrating the emission of fluorescent signal from the nucleus. Interestingly, the signal was found dispersed in the nucleoplasm particularly concentrated around the nucleolus and in structures that resemble nuclear speckles. The distribution within the nucleus observed in this test is reminiscent and consistent with the co localization of both proteins (Figure 3 2A) indicating that RGH3 interacts with U2AF 65 a. To further test the nature of this interaction I co expressed the UHM domain deletion construct (GFP 65 a RFP fusion protein. If the RGH3/U2AF 65 a interaction requires the UHM domain, the co expressed constructs should fail to co zes to the nucleolus and speckles, while U2AF 65 a is dispersed throughout the nucleoplasm (Figure 3 4B). In addition to being diffused in the nucleoplasm U2AF 65 a shows localization to alizes. From these data it can be concluded that RGH3 is able to interact with the splicing factor U2AF 65 a and the RGH3 UHM domain is necessary for this interaction to take place. Moreover, the BiFC data suggest that co localization between RGH3 and U2AF 6 5 a is likely to indicate an interaction. Discussion In metazoans, the process of spliceosome assembly and catalysis of the splicing reaction are well documented (reviewed in Wahl et al., 2009). The lack of a plant in vitro splicing assay has hindered inves tigations of the assembly of the spliceosome and regulation of the splicing reaction. Nevertheless, plants contain homologs of many of


49 animal proteins involved in spliceosome assembly and catalysis (Wang and Brendel, 2004; Lorkovic et al., 2005) arguing fo r a conservation of the constitutive and alternative assembly of the spliceosome and req uire additional enhancing signals recognized by factors such as SR proteins (Long and Caceres, 2009). Due to the variety of pre mRNA existing in an organism and to be able to adapt to changes in cell state or environment, the spliceosome requires participa tion of many loosely associated proteins (Wahl et al., 2009). Interactions between splicing factors and pre mRNA tend to be weak but are enhanced by the collaboration of multiple factors each with weak binding sites (Hastings et al., 2007). These weak inte ractions allow the spliceosome to be a dynamic complex. Interestingly, as demonstrated by its stepwise assembly, not all the proteins associated with the spliceosome participate in every complex. Many of them only aid the proper formation of a specific com plex, are involved in splicing of specific events, or act as a proof read mechanism to help identify vague splicing signals (Wahl et al., 2009). In vertebrates, the U2AF heterodimer complex identifies the Py of the intron, a process tha t leads to the formation of the spliceosome complex E (Wu et al., 1999; Black 2003). Both, small and large subunits the U2AF complex have been identified in plants based on their high structural homology indicating a conserved functional identification o heterodimer. A recently characterized protein in vertebrates, known as PUF60, shows high homology to U2AF 65 and was ab le to substitute U2AF 65


50 dynamic recognition of different and alternative splicing signals by the spliceosome. Similarly, URP interacts with U2AF 65 in vivo and to participate in spliceosome complexes in vertebrates (Tronchere et al., 1997; Shen et al., 2010). I confirmed a conserved interaction of RGH3 and U2AF 65 in planta through co localization and BiFC assays (Figure 3 4) Interestingly, the BiFC interaction takes place in areas within or immediately adjacent to the nucleolus indicating that the re localization of U2AF 65 into the nucleolus observed in co localization assays is not an artifact pr oduced by the high abundance of both proteins. This localization, further suggests the involvement of RGH3 in activities that take place within the nucleolus including post splicing RNA surveillance functions. Based on the observed speckled distribution of the interaction, it can be speculated that U2AF 65 /RGH3 complex forms prior to being recruited to functional sites. Interestingly, though, the localization of U2AF 65 interaction does not occur in nuclear speckles. This suggests that the proteins are stored independently but may be recruited to an additional sub nuclear structure where they form pre spliceosomal complexes reminiscent of the U11/U12 pre spliceosomal complex that in itiates assembly of the minor spliceosome (Frilander and Steitz, 1999; Will et al., 2004) (Figure 3 3B). Furthermore, the conserved UHM domains from U2AF 35 and URP (Figure 3 1) suggest that U2AF 35 and URP interact with U2AF 65 through a similar binding site in the UHM domain. The RGH3/U2AF 65 interaction argues for a conserved URP function in plants and thus may also participate in assembly of the


51 major spliceosome. In humans, U2AF 35 and URP do not overlap functionally indicating that their interaction with U 2AF 65 Interestingly, none of the tested RGH3 protein variants co localize with U2AF 65 (Figure 3 domain and UHM domain, respectively. The absence of co localization with U2AF 65 for both of these proteins suggests that both domains are necessary for interaction yet neither is sufficient. The lack of co localization with the natural protein variants supports the hypothesis that the alternative splicing of Rgh3 results in proteins that are not recruited to the spliceosome. In Fouquet et al. (2011), a quantitative RT PCR assay was designed to amp lify the Rgh3 region between exon 4 and exon 8, where most of the alternative splicing events takes place (see Figure 2 1A), in order to detect and estimate the relative concentration of transcripts coding for multiple Rgh3 isoforms. Due to the extensive a lternative splicing throughout the length of the Rgh3 transcript, the assay did not unambiguously measure versus all other transcripts. However, the relative no mor e than 20% of Rgh3 transcripts suggesting the abundance of the functional Rgh3 transcript is regulated. Overall, the data presented here strengthens the argument that alternative splicing of Rgh3 regulates RGH3 protein l evels which may take place in a de velopmental or tissue specific manner. Materials and Methods Protein Sequence A lignment Predicted protein sequences of URP and U2AF 35 were identified through BLASTP and TBLASTN searches in the National Center for Biotechnology Information databases (http: //, the Joint Genome Institute ( servers,


52 and the p laza plant comparative ge nomics resource (Proost et al., 2009) using default settings at each server. Conserved domains were identified using Prosite scans (http://www at the European Bioinformatics Institute server. Protein sequence alignments were completed with ClustalW2 at the European Bioinformatics Institute server using default parameters ( ): Gonnet protein weight matrix, gap open = 10, gap extension = 0.2, gap distances = 5, no end gaps = no, iteration = none, numiter = 1, clustering = NJ. Subcellular Localization Studies U2AF 65 and U2AF 3 5 coding sequences were extracted from and amplified by RT PCR using normal 14 days old seedling leaf cDNA. N and C terminal protein fusions, as well as agrobacterium transformation and localization analyses were conducted as previously described in the materials and methods section of chapter 2. Vectors for bimolecular fluorescent complementation assays were created by transferring RGH3 and U2AF 65 a cDNA from pENTR vector clones to pSAT4 DEST nEYFP and pSAT5 DEST cEYFP (Tzfira et al., 2005; Citovsky et al., 2006) respectively by LR clonase reaction (Invitrogen). Individual transcription cassettes were digested from cloned vectors with the rare cutte rs I CeuI and I Sce I and ligated into the same pPZP RCS2 binary vector using T4 DNA ligase (Invitrogen) in a stepwise manner. Agrobacterium transformation and transient infiltration procedures were conducted as previously described in the materials and me thods section of chapter 2. Protein expression was visualized 24 to 48 h after transient transformation, and representative


53 images were obtained using a Leica TCS SP5 confocal laser scanning microscope (Leica Microsystems). YFP was excited at 514nm and det ected with an emission band of 525 to 565nm.


54 Figure 3 1. Multiple sequence alignment of the conserved zinc finger UHM zinc finger region of U2AF35 (A) and URP (B) proteins from multiple species. Identical residues are shown in white letters with blac k shading, similar residues are highlighted in gray. Zn fingers and UHM domain are labeled on top of the sequence. Residues involved in intermolecular contacts as previously shown by Kielkopf et al. (2001) are underlined in red. Arg X Phe motif is highligh ted by orange box. The conserved domains were identified within each protein using Prosite scans ( and the sequences were aligned with ClustalW2 using default settings (http://www.e ZmU RP, RGH3 Zea mays ; Os, Oryza sativa ; At, Arabidopsis thaliana ; Hs, Homo sapiens


55 Figure 3 2. RGH3 co localization with U2AF 65 a. A) Individual localization of RGH3 U2AF 65 a, and U2AF 35 a fused to GFP. A ll proteins localize to nuclear speckles but only RGH3 is observed in the nucleolus. B) C o expression of RGH3 RFP with GFP U2AF 65 a demonstrates that both proteins co localize in nuclear speckles (white arrowheads) and disperse in the cytoplasm at potential sites of transcription. Also, U2AF 65 a is re localized to the nucleolus (red arrowhead) due to a potential interaction with RGH3 Lower panel demonstrates overlapping of fluoresc ent signals from a z stack layer of the above image. C) Co localization of U2AF 65 a with U2AF 35 a throughout the cytoplasm indicates that both protein are very likely to interact having a conserved function as that described in metazoans (scale bars = 5m).


56 Figure 3 3. RGH3 truncated protein variants fail to co localize with U2AF 65 a. To test the effect of domain deletions in RGH3 function, three representative RGH3 truncated protein variants ( RGH3 RGH3 and RGH3 ) were fused to GFP and transiently co express with U2AF 65 a RFP in N. benthamiana. Consistent with previous observations, none of the RGH3 pro tein variants are recruited to spliceosomal speckles and are concentrated in the nucleolus (left panels). These proteins fail to co locallize with U2AF 65 a (right panels) which remains concentrated in speckles and disperse in the nucleoplasm (center panels) (scale bars = 5m).


57 Figure 3 4. RGH3 interacts with U2AF 65 a in planta. A) BiFC assays demonstrate the ZMURP interacts with U2AF 65 a in the nucleus. Most samples show fluorescent signal from areas su rrounding the nucleolus (top row), while others emit signal from structures that resemble nuclear speckles (bottom row) Two independent biological replicates were performed confirming the results. B) RGH3 UHM deletion construct fused to GFP fails to colocalize with U2AF 65 a RFP in transient co e xpression assays in N. benthamiana. RGH3 UHM is seen in the nucleolus and nuclear speckles while U2AF 65 a RFP is disperse in the cytoplasm and concentrated in speckles. Interestingly, both proteins seem to localize in different speckles in the cytoplasm (w hite arrowhead) (scale bars = 5m).


58 CHAPTER 4 ANALYSIS OF THE rgh3 umu1 HYPOM O R PHIC ALLELE Introduction Transposable elements (TE) are movable DNA fragments that can insert into new chromosomal locations. These elements often duplicate themselves during transposition to amplify within the genome. Originally discovered in maize by Barbara McClintok, transposable elements are present in almost all studied organisms representing up to 80% of the genome in some species (Feschotte et al., 2002). Eukaryotic TEs are typically organized in two groups based on their mode of transposition: class I elements include all retrotransposons which mobilize via an RNA intermediate; class II elements are transposed as DNA (Hua Van et al., 2005). Both classes are subdivided i nto autonomous elements capable of producing the necessary machinery for transposition and non autonomous elements that require the proteins encoded by an autonomous element in order to transpose. Regardless of the type of element or mode of transposition, TEs are considered to parasitic DNA, transposable elements influence genome size through their ability to self replicate and amplify (Feschotte et al., 2002). Moreover, transposition or homologous recombination between transposon rich areas influences genome organization. TEs also contribute to chromosome form and function by maintaining and regulating heterochromatic areas, where they tend to concentrate, such as centro meres and telomeres (Slotkin and Martienssen, 2007). The mutagenic nature of TEs and their potential effects on gene expression can lead to novel functional variation within a genome. Even though the great majority of transposable elements present in a gen ome


59 are generally inactive, active elements transpose and can insert themselves within or near genic sequences. For example, in maize Class I retroelements greatly outnumber Class II DNA elements. Though, the former are usually clustered in methylated and heterochromatic gene poor areas. On the other hand, DNA transposons are mainly found in unmethylated, genetically active euchromatic regions (Bennetzen, 2000). The activity and function of transposable elements is believed to be the product of an evolution ary adaptation in order for the elements to survive and propagate within a host genome. In principle, a high abundance of transposable elements in gene rich areas could have harmful, deleterious effects on a host genome (Hua Van et al., 2005). Thus, it is in the best interest of both genomes and TEs to alleviate or remove these deleterious effects. Consequentially, many TEs have co adapted by adopting strategies such as transposition bias into non coding regions, excising from exonic sequences through splic ing, or activation in specific tissues (Kidwell and Lisch, 1997). These patterns of transpositions impact on host organisms include the diversification of protein function through introduction of new introns or exons. In maize, a clear example of such an a daptation was recently demonstrated by studies using Helitron mobile elements. Helitrons show a peculiar capability of capturing gene fragments within the element which are then moved as the element moves. Barbaglia et al. (2012) confirmed that the gene fr agments captured by the element are transcribed and demonstrated that through alternative splicing, transcripts containing fragments from different genes are created. Surprisingly, the authors also found transcripts containing joined exons from genes withi n the Helitron and exons in close proximity to the mobile element insertion site. Thus, the Helitrons mobile elements have the ability to create new transcripts that could


60 incl ude Ds alleles of the alcohol dehydrogenase ( Adh) and the ADP glucose glucosyl tranferase ( Wx ). Both alleles contain a Ds element inserted in an exon and encode wild type sized proteins that show an intermediate phenotype when the activator Ac element is not present and Ds cannot transpose (Purugganan and Wessler, 1992). This phenomenon is possible due to the splicing of the Ds element from the pre mRNA. Other evolutionary adaptation include activation of transcription within a TE that affect tr anscription of targeted or nearby genes and influence gene expression in a tissue or developmental specific manner (Girard and Freeling, 1999; Slotkin and Martienssen, 2007). Transposons are useful tools to generate mutants for to the study of molecular biology and functional genomics. In maize, transposable elements have been used as endogenous mutagens in forward and reverse genetic programs to tag and clone genes (Settles, 2009). Transposon tagging uses the sequence of DNA transposons to identify mutag enized genes. The known transposon sequence can be used to enrich for DNA adjacent to the transposon insertion (Brutnell, 2002). Multiple mutagenized populations using a variety of transposable element families such as Ac/Ds En/Spm and Mu exist in maize genes (Brutnell, 2002; Settles, 2009). The UniformMu population, developed by McCarty et al. (2005), harnesses a high mutagenic frequency produced by the high copy number native Mutator element present in maize. The Mutator element is a class II DNA elemen t showing strong insertional bias towards gene rich, non repetitive areas of rough endosperm3 ( rgh3 ) seed mutant was original identified by Fajardo (2008) from


61 the UniformM u population while screening for seeds showing nonautonomous functions in endosperm and embryo development. A Mu insertion within the first exon of a gene coding for a U2AF 35 related protein (URP) was found to be tightly linked to the seed phenotype (Fouqu et et al., 2011). In this chapter, I show that the mapped Mu insertion produces a hypomorphic allele producing a functionally deficient protein that is likely compromised in its ability to participate in spliceosomal complexes. Results Mu transposon Insertion P roduces a r gh3 umu1 Hypomorphic A llele The rough endosperm ( rgh ) class of seed mutants have a typical rough surface to the endosperm that is also termed etched or pitted (Scanlon et al., 1994; Neuffer et al., 1997). A subset of mutan t seeds from the UniformMu population showing a rgh phenotype were screened by B A translocation in order to identify mutants affecting endosperm embryo developmental interactions (Fouquet et al., 2011). The rgh3 mutant became of particular interest becaus e its uncovering crosses suggested that a mutated endosperm negatively impacts wild type embryo development (Fouquet et al., 2011). A Mutator transposable element insertion in the long arm of chromosome 5 was found to be tightly linked with the rgh3 phenot ype; the Mu induced allele was then referred as rgh3 umu1 (Fajardo, 2008; Fouquet et al., 2011). The linked Mu element was inserted within the first exon of Rgh3 coding sequence (see Figure 2 1 for coding sequence scheme). The rgh3 umu1 allele was initiall y believed to be a null allele. However, RT PCR analysis on normal and mutant tissues using Rgh3 specific primers flanking the Mu insertion region amplified a single size shifted band on all mutant tissues when compared to normal (data not shown). Sequenci ng analysis of the RT PCR products revealed the presence of a 141 bp


62 segment of the Mu element terminal inverted repeat (TIR) produced by alternative splicing of the Rgh3 transcript. I performed additional RT PCR amplifications utilizing mutant seedling tissue and cloned and sequence nine full length cDNAs. All nine cDNA clones contained the 141bp Mu element indel fragment formed by junction of a cry p tic donor site found within the Mu element with exon 3 of the Rgh3 transcript. Surprisingly, and even tho ugh the Mu insertion deleted 12 amino acids of the wild type protein, the fragment introduced 47 new amino acids that did not alter the coding frame (Figure 4 1). Interestingly, eight out of the nine clones were predicted to code for a full length protein similar to RGH3 (Figure 4 1), while the remaining product could code for a protein similar to RGH3 These data argues that rgh3 umu1 is not a null allele but rather a hypomorphic allele. The unexpected low abundance of transcripts coding for RGH3 trunca ted proteins in mutant tissues argues that the Mu insertion may somehow interfere with the alternative splicing mechanism that give raise to alternatively spliced isoforms in normal Rgh3 tissues. Interestingly, a similar example where a Mu insertion alters the splicing pattern of a transcript was previously observed in two mutant alleles of the maize Alcohol dehydrogenase1 ( Adh1 ) gene (Ortiz and Stromer, 1990). Moreover, another UniformMu seed mutant identified in our laboratory shows the exact same Mu elem ent splicing pattern observed in rgh3 umu1 (Jeffery Gustin, unpublished data). RGH3 umu is Found in vi vo a nd S hows Partial C o localization W ith U2AF 65 To test if the rgh3 umu1 transcript codes for a protein in vivo, I extracted protein from no r mal and mutant 24DAP seeds, and modified and unmodified mutant seedling (see Chapter 5 f or details on mutant seedlings). Western blots were then probed with


63 the a nti RGH3 N terminal peptide antibody which detect ed bands of similar sizes in the normal as well as th e mutant seed tissues (Figure 4 2A). From the data presented in chapter 2, the heaviest band in normal tissues ( 125kDa) belongs to RGH3 This indicates that the band of similar size detected in mutant seed tissues probably is RGH3 umu Surprisingly, and contrary to what was observed in Figure 2 2, the C terminal antibody did not detect the bands is see tissues Similarly, t hese proteins were not detected in mutant seedling tissues either. To confirm translation and size of RGH3 umu I also cloned the rgh3 umu1 sequence and express it in vitro using wheat germ extracts Proteins were detected with the same N and C terminal anti RGH3 antibodies. As demonstrated by the blotted membranes shown in Figure 4 2B, rgh3 umu1 produces a protein that is similar in si ze to RGH3 and is detected with both antibodies. The results indicate that RGH3 umu is being produced and that the amino acids introduced by the Mu electromobility As mentioned in chapter 2, technical diffi culties in the protein extraction step and western blot analyzes prevented further experiments to confirm these results. To determine the functional consequences of the RGH3 umu protein sequence, I fused RGH3 umu to GFP to examine the sub cellular localization of the protein by transient expression analysis in N. benthamiana In Figure 4 3A, RGH3 umu localizes to the nucleolus and is also disperse in the nucleoplasm. Data from three independent biological replicat es indicate that the recruitment of RGH3 umu to nuclear speckles is impaired when compared to normal RGH3 protein. In chapter 3, the normal RGH3 protein is shown to interact with U2AF 65 in vivo (Figure 3 4). To determine if the RGH3 umu protein also inte racts with U2AF 65 I


64 performed co localization studies between GFP RGH3 umu and U2AF 65 a RFP fusion proteins in N. benthamiana RGH3 umu is able to partially co localize with U2AF 65 a but not as readily as the normal RGH3 (Figure 4 3B). Moreover, RGH3 umu d oes not always co localize with U2AF 65 (Figure 4 3C) and frequently shows a non overlapping signal similar to that of RGH3 truncated protein variants (Figure 3 3). These data argue that the hypomorphic RGH3 umu protein is likely to be functional but not to the same extent as a normal RGH3 protein. The Mu insertion may also affect protein turnover or expression as suggested by the relative to normal RGH3 Combined, these data suggest the Mu insertion causes altered subnuclear localization and reduced RGH3 protein function. Rgh3 is Required For a Subset of RNA Splicing E vents In human cells, URP participates in both U2 and U12 splicing and is essential for cell culture survival (Tronchere et al., 1997; Shen et al., 2010). In maize, I showed that RGH3 intera cts with U2AF 65 a, suggesting an orthologous role in splicing between humans and maize. To determine whether RGH3 umu alters splicing, we selected 21 maize genes that are alternatively spliced in maize, Arabidopsis, and rice (Wang and Brendel, 2006b; Table 4 1). I performed semi quantitative RT PCR assays with RNA from normal and mutant tissues to compare splicing patter ns (Figure 4 4). Only three genes had differences in isoform usage in rgh3 umu1 and wild type tissues. GRMZM2G165901 encodes a Gly rich RNA binding protein with two major splice variants (Figure 4 4A). Sequencing of these isoforms found a noncanonical intr on retention with GU CG dinucleotides at the 59 and 39 splice sites instead of GU AG. The rgh3 mutation reduces the level of intron retention in seed and seedling tissue,


65 suggesting noncanonical splicing is more efficient in the mutant. The smaller variant contained different splice junctions in rgh3 and the wild type with rgh3 shifting the splice acceptor site by three bases. GRMZM2G051276 encodes a putative inositol monophosphatase with three splice variants (Figure 4 4B). Sequencing of these variants fou nd complex alternative splicing within annotated intron 10. First, a four base exon is found that results from splicing of two noncanonical introns with UU AA and AU UU dinucleotides. Second, an alternative variant contains only a single intron between the annotated exons 10 and 11. Assuming the same donor site is used in the alternative variant, the dinucleotides for the predicted intron are UU UU, indicating this intron is also noncanonical. Relative to the wild type, the alternative, retained intron vari ant accumulates to higher levels in rgh3 seed tissue but to lower levels in endosperm culture. GRMZM2G081642 encodes a protein of unknown function, which is conserved within plants and algal species. Sequencing of four variants identified an alternative do nor site for intron 2 in which the shorter variant is a GC AG intron (Figure 4 4C). The longer variant splices with a canonical GU AG intron, and the rgh3 tissues have higher levels of this canonical donor site. Intron 3 has three alternative acceptor site s that all have canonical dinucleotides. Combined, these data suggest that RGH3 modulates splice site selection for a subset of non canonical introns. Furthermore, the data further strengthen the argument that RGH3 umu function is variable but not inhibit ed Discussion Transposable elements are exceptional mutagenic agents capable of affecting individual genes as well as whole genomes (Bennetzen, 2000). The ability of TEs to


66 move about the genome inactivating or altering gene expression has become an essen tial tool for molecular and functional genomic studies in maize (Settles, 2009). In fact, over the last few years efforts to harness the properties of TEs as mutagenic tools have resulted in the creation of multiple large scale mutagenesis collections tha t mostly utilize Ac/Ds or Mutator elements (May et al., 2003; Fernandes et al., 2004; Kolkman et al., 2005; McCarty et al., 2005; Ahern et al. 2009). The Mutator ( Mu ) transposable element is an ancient element and is regarded as the most mutagenic plant tr ansposon studied to date (Brutnell, 2002; Lisch, 2002). Mu transpositions have the tendency to occur to single copy or low copy number Additionaly, Mu elements have the ability to move to any chromosome in the genome making it the ideal genetic tool for mutagenesis projects (Xia Min and Lisch, 2006). The general assumption is that Mu elements, or other TEs, create null alleles of genes upon tional importance through altered plant phenotypes. Nevertheless, multiple examples in maize have demonstrated that Mu elements are capable of influencing gene regulation post transcriptionaly or post translationaly exposing interesting molecular features of TEs as well as the targeted gene (reviewed in Girard and Freeling, 1999; Weil and Wessler, 1992). The rgh3 umu1 hypomorphic allele is yet another example of how Mu elements can alter gene expression or protein function. Together with the Adh1 S3034 alle le (Ortiz and Stromer, 1990), rgh3 umu1 is the second published example showing a conserved splicing pattern. Moreover, our lab recently found an additional example arguing that this event is a more general phenomenon rather than isolated events. Taken tog ether, these


67 events involving Mu elements argue that this active TE has been able to survive by decreasing its deleterious impact on the host genome and potentially increasing protein diversity. Moreover, as explained in Fouquet et al. (2011), the hypomorp hic rgh3 umu1 allele reveals the developmental importance of Rgh3. This insight might not have been possible if rgh3 had been null allele due to a probable gametophytic lethal phenotype. In conclusion, the data suggest that Rgh3 may be required in importan t seed and seedling developmental functions in maize. Most importantly, they demonstrate that the effect of this type of Mu insertion could enhance the study of alleles with fundamental implications in development and that typically are knock out lethal. P reviously, I demonstrated that RGH3 interacts with the U2AF 65 protein through the UHM domain (Figure 3 3), a behavior consistent to that observed in humans (Tronchere et al., 1997; Shen et al., 2010). Moreover, even though its function has not been extens ively analyzed in humans, data obtained from analyses with RGH3 natural isoforms demonstrate that the RS domain of RGH3 enhances nuclear localization and is required for recruitment of the protein to spliceosomal speckles and complexes. Based on studies in vertebrates, the RS domain of U2AF 35 is required for protein protein interactions with splicing factors of the SR family in order to accurately identify rgh3 umu1 hypomorphic allele codes for a full length RGH3 umu with an additional 47 aa in the acidic domain, partially retaining its ability to participate in spliceosomal complexes. Nevertheless, rgh3 umu1 is seed and seedling lethal, indicating that the RGH3 aci dic domain is also necessary for protein function. Even though I can only speculate about its function, it is possible that the acidic domain enhances protein protein interaction with U2AF 65 or with


68 an additional splicing factor to strengthen the recogniti on of splicing signals. As indicated by studies on the human splicing factor SFSR1 (Cho et al., 2011), regulatory domains of a protein can mask or expose additional functional domains in order to regulate participation of the protein in complexes. Thus, an additional function of the acidic domain could be to regulate the ability of RGH3 to form protein protein complexes by masking the UHM domain or by regulating the function of the RS domain. Finally, despite the severity of the rgh3 umu1 mutant phenotypes, alternative splicing events are not severely disrupted in rgh3 umu1 tissues. This indicates that RGH3 is involved in only a few essential regulatory splicing events (Figure 4 4). In plants, similar examples of developmental abnormalities produced by knock down and misexpression alleles of U2 and U12 specific splicing factors have been observed previously (Kalyna et al., 2003; Wang and Brendel, 2006; Ali et al., 2007; Kim et al., 2010). Likewise, overexpression of proteins involved in splicing have also sho wn a range of pleiotropic effects that can negatively impact plant development (Lopato et al., 1999; Kalyna et al., 2003). Consequently, proper tissue or developmental regulation of essential splicing factors is crucial to ensure adequate protein expressi on levels and proper plant development. Poor regulation, expression, or stability of the RGH3 umu protein likely compromises its function and causes abnormal seed development. In conclusion, the data suggest that the hypomorphic allele rgh3 umu1 may not be a rare allele produced by the alternative splicing of the Mu element, exposing a likely adaptation of this element for its continual survival within the maize genome. Furthermore, the lethal nature of the rgh3 umu1 phenotype indicates that the acidic


69 doma in of RGH3 is necessary for proper protein function in the regulation of a reduce set of alternative splicing events. Materials and Methods In vitro Transcription/Translation and Western Blot Analysis of RGH3 P roteins Rgh3 and Rgh3 umu1 transcripts were cloned and tested as previously described in the materials and methods section of chapter 2. Subcellular L ocalization Studies Rgh3 umu1 transcript was cloned and tested as previously described in the materials and methods section of chapter 2. RT PCR Analyses of Alternatively Spliced Maize G enes Gene candidates were selected from a large list of genes found in the Alternative Splicing in Plants database (ASiP, Wang and Brendel, 2006b) All genes showed alternative splicing evidences in Arabidopsis and R ice. Selected g enes were blasted against the Maize reference genome ( ). Repetitive g enes genes with no orthologous in Maize, or genes that are member of a large family were discarded. ESTs from remaining genes were then analyzed for evidences of alternative splicing. In the end, 22 genes were selected for RT PCR analysis. Total RNA was extracted from multiple maize normal and rgh3/rgh3 tissues as describe d by Reid et al. (2006) using 10 mL of extraction buffer/gr of fresh weight. RT PCR was performed on first strand cDNA and synthesized by Superscript III (Invitrogen) using gene specific primer sets described in table 4 1. Amplified fragments were visualiz ed by electrophoresis on 2% agarose gels (0.5x TBE) and stained in ethidium bromide solution ( 0.1 g/mL).


70 Figure 4 1. Multiple sequence alignment of RGH3 protein isoforms and mutant allele. Greek letters indicate wild type isoforms, RGH3 umu1 length protein product of the rgh3 umu1 allele. The nuclear localization signal is highlighted in blue. The zinc finger domains are highlighted in green, and the UHM domain is in white letters with black shading. R esidues that are not were identified with Prosite scans ( The sequences were aligned with ClustalW2 using default settings ( ).


71 Figure 4 2. rgh3 umu1 allele produces a full length protein of comparable size to RGH3 protein. Western blot analyses of tissue protein extract (A) and in vitro reactions (B) detected with N terminal (left panel) or C terminal (r ight panel) anti RGH3 antibody A) The N terminal Ab detects multiple bands in both normal and rgh3 seed tissues. On the contrary the C terminal Ab only detects a single band at 5 6 kDa. A single small band was detected in rgh3 Open seedling by the N terminal Ab B) in vitro expressed proteins are of similar size at 125kDa and are detected with both Ab indicating production of a full length protein RGH3 umu that is found in mutant tissue. Each panel shows two images from a same western blot membrane processed to facilitate comparison between samples.


72 Figure 4 3 RGH3 umu is recruited to speckles and partially co localizes with U2AF 65 a. RGH3 umu was fused with GFP and analyzed through transient expression in N. benthamiana by itself (A) or with U2AF 65 a RFP (B C). A) Multiple experimental replicates demonstrate that RGH3 umu is consistently found in the nucleolus but transiently localizes to nucle ar speckles and not as readily as RGH3 (white arrowhead). B C) The hypomorphic protein partially co localizes with U2AF 65 a in the nucleoplasm (red arrowhead) but not in the nucleolus (B). The co localization between the two proteins was rarely present and often times no co localization was observed (C) (scale bar = 5m).


73 Figure 4 4 RNA splicing defects in rgh3 detected with semi quantitative RT PCR Schematics show intron exon structures as determined by cloning and sequencing of the RT PCR products. Exons are numbered according to the B73 annotation of release 5b.60. Black boxes indicate retained intron sequences. A) GRMZM2G165901 has a novel splice acceptor site in rgh3 with three additional bases included in the mutant intron (white box). B) GRMZM2 G051276 has a four base exon between annotated exons 10 and 11. The retained segment of annotated intron 10 also shifts the splice acceptor sequence by two bases relative to the 4 base exon. C) xon 2 and




75 CHAPTER 5 MAPPING OF THE rgh3 SEEDLING GENETIC MOD IFIER AND THE dek*9700 LOCUS Introduction The maize Rough endosperm3 ( Rgh3 ) gene shows significant homology to the human URP splicing factor The human gene was shown to be required in splicing activities in vitro interact with U2AF 65 and participate in both U2 and U12 type s pliceosomal complexes (Tronchere et al., 1997; Will et al., 2004; Shen et al., 2010). Originally identified by Fajardo (2008), the maize rgh3 mutant affects seed and seedling development. In seeds, the rgh3 allele shows a range in the severity of seed phen otype which includes cell differentiation defects for basal endosperm transfer cell layer (BETL) and the embryo surrounding region (ESR) (Fouquet et al., 2011). About 50% of rgh3 seeds are able to germinate in soil, which correspond to the heaviest, least severe class of seed phenotype. However, rgh3 seedlings are lethal at about 15 days after germination. Surprisingly, mutant endosperms are able to proliferate more readily than normal endosperms in tissue culture indicating that Rgh3 is required to repress cell proliferation (Fouquet et al., 2011). I showed that rgh3 umu1 is a hypomorphic allele and that a small number of alternative RNA splicing events are affected in the mutant. Moreover, I found that Rgh3 transcript is alternatively spliced and that RGH3 protein is able to interact with U2AF 65 consistent with the behavior of human URP. Taken together, the data strongly indicate that RGH3 is the ortholog of human URP. The rgh3 umu1 allele provides a unique protein variant that can identify the targets an d interacting proteins that are most sensitive to altered URP/RGH3 function. These gene targets or interacting proteins are expected to help explain the rgh3 umu1 phenotype and give insight into the function of the RGH3 acidic domain.


76 Maize ( Zea mays ) is a highly diverse plant species. It comprises several hundred inbred lines as well as landraces showing a tremendous level of variation in morphological traits as well as polymorphism at the DNA level. Maize is thought to come from a single domestication eve nt (Matsuoka et al., 2002), yet the level of genotypic variation translates into a rich source of natural allelic variation that can modify mutant phenotypes. Inbred or landrace genetic modifiers can sometimes be the product of multiple factors, or the eff ect of single genes, which interact or are targets of a mutant locus (Lopes et al., 1995; Vollbrecht et al., 2000). Map based or positional cloning is a robust approach to uncover the genetic cause of a phenotype. Positional cloning of mutants from defined genetic backgrounds can be simplified relative to mapping from undefined or mixed backgrounds (Jander et al., 2002). The first step of positional cloning is identifying a map position to bin level resolution. This is most efficiently done using a core set of distributed markers (Bortiri et al., 2006). The two most widely used molecular marker systems in plant breeding and genetics are SNPs and SSRs (Appleby et al., 2009). In contrast to SNPs, SSRs are more amenable to small scale experiments such as a mapp ing a single mutant using bulk segregant analysis (BSA) (Gallavotti et al., 2008; Thompson et al., 2009). Individual SSR markers can be more easily added or removed from a mapping experiment and a smaller number of samples are generally analyzed. The cost of SSR mapping can be further reduced by identifying marker sets that are most useful for the specific mapping experiment. BSA mapping requires co dominant markers. The Maize Mapping Project characterized hundreds of SSRs and deposited images of inbred scr eening gels on the MaizeGDB database (Sharopova et al. 2002). These screening


77 gels included F 1 or mixed DNA samples to test for co dominant alleles for only 1 2 inbred pairs of the 11 inbreds screened. Similarly, Fu et al. (2006) developed and characterize d insertion deletion polymorphism (IDP) markers within 24 inbreds but did not screen mixed or F1 DNA samples. In addition, the IDP markers were not screened for the predominant inbred used in public mutagenesis projects, W22. Our anecdotal experience sugge sted that size differences in SSR alleles were not sufficient to predict co dominant markers. The rgh3 umu1 allele was originally isolated in the maize W22 background. Though, when crossed into other inbred backgrounds such as B73 or Mo17 a modified seedli ng phenotype was observed. I decided to identify the seedling phenotype genetic modifier locus through a map based cloning approach. In order to make the mapping more efficient, and due to the above mentioned issues, I analyze 505 SSR markers for co domina nt polymorphisms between the B73, W22, and Mo17 maize inbred lines to identify a distributed marker set. The distributed marker set allows efficient mapping of mutants from B73 and W22 public mutagenesis experiments. The effectiveness of the marker set was further demonstrated by the cloning of a dek mutant ( dek*9700 ) from the UniformMu mutagenesis population (McCarty et al., 2005) by BSA. Results A D ominant rgh3 Seedling Modifier is Present in the B73 Maize I nbred To facilitate the mapping of the Mu element linked to the rgh3 mutant phenotype, several F 2 mapping populations were generated in maize inbred backgrounds including B73 and Mo17 (Fajardo, 2008) In the B73 F 2 the normal to mutant seed ratio deviated from an expected 3:1 to about 15:1. In t he W22 background, a fraction of mutant seeds germinate and exhibit aberrant development with adherent, narrow leaves resulting in


78 hooked seedlings that died 15 to 18 days after planting (Figure 5 1). Interestingly, mutant seedlings in F 2 populations from crosses to B73 also showed stunted growth but were characterized by an open, round leaf morphology (Figure 5 1). Due to the unexpected low frequency of mutant seeds, I decided to plant normal looking seeds to test for the presence of rgh3/rgh3 seedlings in this population. Both types of mutant seedlings, open leaves or the adherent, hooked phenotype were observed. The distortion of the normal to mutant seed ratio as well as the observed difference in seedling phenotype suggests the presence of genetic modif iers of rgh3 in the B73 background. To test this hypothesis, at least at the seedling level, I back crossed segregating F 1 progeny from a B73 X rgh3/ + cross with a rgh3/ + W22 tester parent line to create a BC 1 population (Figure 5 2A). Seeds from six segre gating ears were separated between normal and mutant groups and 148 rgh3/rgh3 seeds were planted. About 55% of the seeds germinated and their seedling phenotypes were scored (Table 5 1). The phenotypic difference between modified looking seedlings was name d open, and unmodified was referred as adherent. The modified phenotype showed a gradient in severity (Figure 5 2B). Consequently, seedlings were grouped into two main categories, open or adherent, which were then sub divided between a high and low confid ence phenotype (Table 5 1). Overall, the final ratio between both seedling phenotypes was close to 1:1, which suggests a single dominant seedling modifier from the B73 parent. In order to map this modifier locus, I needed molecular markers for mapping in B 73 and W22 inbred parents. Development of a Distributed SSR Marker S et Each of the 505 SSR markers was tested for co dominant polymorphisms between B73/Mo17, B73/W22, and Mo17/W22. A co dominant marker was defined as useful for


79 F 2 mapping when it amplified easily resolved size polymorphisms between at least two inbreds and showed a novel banding pattern in a 1:1 mix of a pair of inbred DNA samples (Figure 5 3A, umc1538). Based on these criteria, 238 (47.1%) of the markers amplified co dominant markers with each pair of inbreds having 154 170 useful markers (Figure 5 3B; Table 5 2). Less than 10% of the 505 markers had three distinct alleles for the inbreds, such as umc1538 (Figure 5 3A). 31.9% of the markers had two alleles, while 8.5% of the markers showed co dominance in just one of the three inbred pairs. The remaining 267 markers that were not useful for BSA gave the following amplification patterns: 76 amplified a single allele in all inbreds (Figure 5 3A, umc1288); 129 amplified alleles that were diffic ult to resolve or score (Figure 5 3A, umc1590 and phi402893); and 62 failed to amplify. I selected a distributed, co dominant marker set that could be used for all of the inbred pairs. For this analysis, I divided the IBM2 2008 Neighbors map coordinates by a factor of 4 to account for the genetic expansion of the IBM population (Lee et al., 2002). This is the average conversion factor for marker coordinates between the Genetic 2008 and IBM2 2008 Neighbors maps at MaizeGDB. Using these predicted genetic dist ances, the average distance between all polymorphic markers for each inbred pair was <14 cM (Table 5 2). A minimally redundant set of distributed markers would be spaced at 50 cM intervals to ensure that all phenotypic variations can be detected by at leas t one marker. Based on the size of the IBM2 2008 Neighbors map, 50 markers would be needed for a minimal distributed set. However, only 43 markers that contained three distinct alleles in B73, Mo17, and W22 were observed and these markers are not distribut ed uniformly. To account for these issues, I selected a distributed set of 85


80 markers that includes some redundancy (Figure 5 4). 64 71 of the distributed markers are polymorphic for each inbred pair, and these polymorphic markers are spaced at a mean gene tic interval of 27 29 cM (Table 5 2). The distributed markers contain some gaps in which the closest marker is >25 cM (Figure 5 4). The majority of the gaps in coverage are at the ends of chromosomes with the largest gap located on the long arm of chromoso me 8. This gap is likely to be caused by an error in the IBM2 2008 Neighbors map. The terminal locus of this arm is annotated as Empty pericarp4 ( Emp4 ) and adds approximately 46 cM of genetic distance to the map. Emp4 has been mapped to chromosome 1 via tr anslocations, molecular markers, and molecular cloning (Gutierrez Marcos et al., 2007). After excluding the Emp4 locus from the map, 7.3 9.6% of the genome is predicted to be located >25 cM from a marker depending upon the inbred pair (Table 5 2). Mapping of rgh3 Seedling Genetic M odifier To map the genetic modifier of rgh3 seedling phenotype, I expanded the BC 1 mapping population to increase the number of meiotic products available for testing by BSA. Mutant seeds, and also seeds from the normal looking gr oup were planted and genomic DNA was extracted from germinated mutant seedlings. I ndividual DNAs from adherent and open rgh3/rgh3 seedlings were pooled by groups based on their phenotype. Both DNA pools were tested with the distributed marker set under ide ntical PCR conditions along with a control 1:1 mix between W22:B73 DNA. Since the population was back crossed to the W22 parent but the modifier is dominant in the B73 background, modified open individuals should be heterozygous at the modifier locus. Thus an increased number of markers should become heterozygous in the modified open DNA pool as they map closer and become linked to the modifier location. The


81 adherent DNA pool should show the inverse distortion towards W22 for the same markers indicating ab sence of the domain modifier allele. Out of all tested markers throughout the genome, markers mapping to the short arm of chromosome 9 showed the most distortion towards B73. Therefore, I began fine mapping analyses with individual DNA samples and tested t hem with SSR markers showing distortion in that area. A marker located at 13.2Mb and at 5.3Mb (umc1170 and umc1867, respectively) indicated B73 allele enrichment towards the proximal end of the chromosome (Figure 5 5A). To analyze the complete area, I de signed and tested additional SSR markers at 0.5, 8.2, 9.7, and 10.9Mb. Enrichment for the B73 allele was observed in the segment between markers located at 8.2 and 10.9Mb indicating mapping of the modifier locus (Figure 5 5B). All three markers in the regi on showed very similar recombination frequencies preventing fine mapping. Mapping of dek*9700 from UniformMu P opulation To test the effectiveness of the distributed set to map a mutant allele from public mutagenesis population, I completed BSA for the dek*9700 mutant from the transposon tagging UniformMu population developed at the University of Florida (McCarty et al., 2005). Ideally, this mapping experiment should also to test the reliability in which a marker can detect different allele in a mixed DN A F 2 background and if this information is enough to distinguish between a linked versus an unlinked marker. That is, it will demonstrate if the alleles from markers in the distributed set can accurately be distinguished when the marker is linked to a locu s of interest. Then, to complete the mapping experiment, I tested Mo17/UniformMu and B73/UniformMu F 2 mapping populations and found segregation distortion on chromosome 6 in both populations.


82 PCRs of dek mutant individuals from the Mo17/UniformMu populatio n were used to refine the map position (Figure 5 6A). Some of the dek mutant kernels in this experiment were exceptionally small, and I extracted DNA from whole dried kernels. Surprisingly, these had relatively little maternal DNA contamination, and recomb inants could be scored with reasonable confidence (Figure 5 6A, lanes 34 45). These experiments mapped the dek mutation to a 10.6 cM interval between umc1063 and umc1653 (Figure 5 6B). The predicted genetic distance between these markers is 20.5 cM suggest ing that the conversion factor between IBM2 2008 Neighbors map and the Genetic 2008 consensus map coordinates may be an underestimate. We scored the mapping population for bnlg345 to obtain additional recombinants. When bnlg345 is included, the total inter val observed between bnlg345 and umc1653 is similar to the expected distance with 32.3 cM observed versus 39 cM expected. These data suggest the IBM 2008 Neighbors map provides accurate map distance estimates when the W22 inbred is used as a mapping parent This mapping experiment was able to place the dek* 9700 mutant isolate to an approximately 10 cM interval in bin 6.07 indicating that the markers provide a robust resource for mapping UniformMu mutants. Discussion The maize RGH3 protein is the homolog of human URP, a protein involved in assembly and function of the U2 and U12 spliceosome (Tronchere et al., 1997; Shen et al., 2011) Rgh3 is required for proper endosperm embryo development in the maize seed by influencing endosperm cell differentiation (Fou quet et al, 2011). Identifying additional protein interactors and/or target genes could greatly enhance our ability to understand the biochemical processes that are most sensitive to reduced Rgh3 function. Genetic modifiers can provide valuable information towards understanding the


83 biochemical bases of the trait (Lopes et al., 1995; Vollbrecht et al., 2000) Maize is a highly diverse organism providing a vast array of natural genetic variation that can be used to identify genetic modifiers. The hypomorphic rgh3 umu1 allele was originally discovered in the W22 background where it shows a variable range in seed phenotype (Fajardo, 2008). Interestingly, when crossed into the maize B73 inbred background, the seed phenotype becomes partially suppressed an d the se edling phenotype has an open, rounded leaf morphology (Figure 5 1). Through mapping experiments using a distributed SSR marker set I was able to localize the modifier loci to a 3Mb region on the short arm of chromosome 9 (Figure 5 5B ). Further fine mapping was not possible due to conflicting recombinant individuals in the open and adherent phenotypic classes, which is possibly due to the range of seedling phenotypes. Overlap between the expressivity of the B73 and W22 phenotypes may l ead to scoring errors and mis assignment of individuals to the incorrect genotypic class. Mis assignment of open and adherent genotypes would decrease the resolution within the linkage region. The specific cause of the variable, modified seedling phenotype s is not known. It is possible that the hypomorphic rgh3 umu1 allele contributes to the modified seedling phenotype range. In the W22 background, rgh3 umu1 shows a variable range of phenotypes and I have shown that the RGH3 umu1 protein also has variablesu b nuclear localization as well as variable levels of co localization with U2AF 65 .. Alternatively, the variability could be produced by the modifier locus rather than the RGH3 umu1 protein. However, the seedling phenotype variability was also observed in ad vanced back crossed populations, such as BC 4 where the background is almost entirely W22 (data


84 not shown) supporting the idea that variability in RGH3 umu1 function is the more likely cause of the observed range in seedling phenotype. One possible approac h to obtain a higher resolution map position for the rgh3 modifier would be to use the extreme or high confidence open and adherent seedling phenotypes. Currently, the available number of meiotic products in the high confidence groups is too few to improve resolution. It would be necessary to expand the mapping population to increase the number of available high confidence meiotic products. However, the time and effort required to generate the larger population would make the approach inefficient to clone t he locus. Other approaches are possible to find targets and interacting proteins, such as protein complex pull down assays or RNA immunoprecipitation assays. These biochemical approaches are more likely to provide mechanistic information in a more cost eff ective manner. The development of common mutagenesis resources in the B73 and W22 inbreds creates the opportunity for map based cloning in well defined genetic backgrounds. By using defined inbreds, a smaller number of markers can be selected to ensure tha t mutants are mapped in a BSA (Liu et al. 2009). A SNP marker system has been developed for BSA mapping of maize mutants. The authors recommend 1,016 markers be used for mapping mutants in uncharacterized inbred combinations such as those involving W22 (Li u et al. 2009). The large number of markers required, high initial set up costs, and requirement to complete hundreds of BSA mappings before SNP genotyping becomes cost effective makes this technology less accessible for small research groups that are inte rested in mapping a few mutants at a time. Consequently, I focused on


85 identifying distributed markers with technology that is more suitable for lower throughput genotyping. Despite the large number of maize molecular markers already developed and character ized, it is not simple to identify distributed, co dominant markers for pairs of inbreds. The presented data suggest approximately 30% of mapped SSRs will be useful for BSA of any given pair of divergent inbreds. This is twice the frequency at which maize SNP markers are expected to produce quantitative co dominant markers for a pair of divergent inbreds (Liu et al. 2009) and is consistent with the higher information content of SSR loci (Hamblin et al. 2007). It is important to note that the analysis was re stricted to 4% TBE agarose gel electrophoresis. An additional 25% of the markers analyzed in this study amplified products that could potentially be scored using higher resolution agarose and capillary electrophoresis techniques. The distributed markers I selected provide a simple marker technology to enable mapping of mutants from public mutagenesis resources. By surveying for W22 polymorphisms, mutants from multiple public transposon mutagenesis populations and one EMS mutagenesis population can now be ma pped more readily (Cowperthwaite et al., 2002; Till et al., 2004; Kolkman et al., 2005; McCarty et al., 2005; Ahern et al., 2009). Although I was not able to precisely localize the rgh3 modifier locus, the usefulness of the marker set was demonstrated by m apping the dek* 9700 mutant isolate to an approximately 10 cM interval in bin 6.07. Two seed mutants, su2 and dek* 1104 have recombination data that place these loci >20 cM proximal to dek* 9700 (Scanlon et al. 1994). Nine other seed mutant isolates inclu ding 2 named loci, dek19 and emb3 have been mapped to the long arm of chromosome 6 using B A


86 translocations (Chang and Neuffer 1994; Scanlon et al. 1994; Neuffer and England 1995; Heckel et al. 1999). Complementation tests with dek19 and emb3 will be need ed prior to assigning dek* 9700 a locus name. Finally, I estimate that 7.3 9.6% of the genome, depending on the inbred combination, is likely to be outside the range of the distributed marker set to detect linkage in a BSA. Thus, it is expected that 90 93% of mutants should be able to be mapped with a single F 2 mapping population using the marker set reported here. However, segregation distortion for many SSR markers is readily apparent when one allele constitutes 75% of the DNA sample (Carson et al. 2004; Jones et al. 2007), which corresponds to a Haldane genetic distance of 35 cM. Assuming this upper bound is a realistic expectation for BSA, the coverage of the distributed markers will be greater and the success rate in using this marker system should appr oach 96 98%. The frequency of success could be increased further by generating two F2 populations with crosses between all three inbreds. Materials and Methods Plant M aterial Back crossed mapping populations were designed as described by scheme on figure 5 2. Seeds from BC 1 progeny from rgh3/+ W22 tester x F 1 crosses (figure 5 2) were scored visually for normal or rgh3/rgh3 phenotype and were then planted in soil under controlled conditions. Two week old mutant seedlings were scored for open or adherent ph enotypes and DNA was extracted from seedling leaf as described by Settles et al. (2004). For BSA analysis, samples were pooled to create open and adherent bulks. Individual DNA was tested with linked SSR markers under identical conditions described below a nd recombinants were scored. For SSR markers testing, genomic


87 DNA from the B73, W22, and Mo17 inbreds was extracted from 2 week old seedlings as described (Settles et al., 2004). The proof of concept mapping experiment was completed by crossing a UniformM u defective kernel ( dek ) isolate, dek* 9700 to the B73 and Mo17 inbreds. F 2 mapping populations were generated by self pollinating F 1 plants. Mature mutant and normal seeds were selected visually from segregating ears of the B73/UniformMu and Mo17/Uniform Mu populations. For DNA extraction, the seeds were imbibed in water overnight, and the pericarp was removed. For normal seeds, the embryo was dissected for the extraction. For the dek mutant seeds, the entire endosperm and embryo was used in reduced grain fill mutants. In the Mo17/UniformMu population, 11/42 dek kernels had very severe grain fill defects, and the pericarp was included in the DNA extraction for these kernels. DNA extraction was completed as described (Settles et al., 2004), except that 1 mL of extraction buffer was used and the homogenized sample was centrifuged prior to phenol:chloroform:isoamyl alcohol extraction. This step sedimented the starch gel formed by the DNA extraction buffer. The supernatant was transferred to a new microcentrifug e tube prior to completing the remaining steps of the extraction. For the BSA PCR, the individual samples were pooled to create normal and mutant bulks. The samples were amplified with the distributed marker set. Individual mutant DNA samples were tested b y PCR with the linked SSR markers, and map SSR Testing and S coring Purified DNA was diluted to a concentration of 20 ng/L just prior to PCR. Each SSR marker was amplified from the th ree inbreds and from 1:1 mixes of B73/W22,


88 Mo17/W22, and B73/Mo17 DNA. SSR markers were tested from a commercial primer set of 480 primer pairs with 477 non redundant markers (M8818 1SET, Sigma Aldrich Co., St. Louis, MO). The remaining 28 primer pairs wer e selected to fill gaps in the distributed sets from the IBM2 2008 Neighbors Frame 2 genetic map at the MaizeGDB database ( ). Primer sequences for these markers are available at MaizeGDB. Each ma rker was tested under common PCR conditions (0.25 M primers, 150 M each dNTP, 40 ng DNA, and GoTaq PCR mix, Promega Co., Madison, WI). Thermocycling conditions were 94C for 40 s, 57C for 45 s, and 72C for 40 s with 34 cycles. Amplified fragments wer e visualized by electrophoresis on 14 cm, 4% agarose gels (0.5% TBE) at 90 V for 2h and stained in ethidium bromide solution ( 0.1 g/mL). Co dominant polymorphisms were scored visually from the gel images. If a marker failed to amplify or gave multiple p roducts within an inbred DNA, the PCR was repeated 2 3 times to confirm the amplification pattern.


89 Figure 5 1. Abnormal rgh3 seedling phenotype on multiple maize genetic backgrounds. rgh3 umu1 was isolated in the W22 maize inbred background and was crossed to B73 inbred to create mapping populations (left panel scheme). In W22 background, the rgh3 seedling phenotype is characterized by an stunted growth, and adherent, hooked leaf morphology. Wh en crossed into B73 inbred, a modified seedling showing stunted growth, open leaf morphology was observed (images on the right).


90 Figure 5 2. Gradient of abnormal rgh3 seedling phenotype. A) Left panel scheme shows crossing design to create introgress ions of lines segregating for the modifier loci into a W22 rgh3 /+ tester line B) Gradient of abnormal rgh3/rgh3 seedling phenotypes observed in BC 1 population. Adherent denotes unmodified phenotype; open denotes modified phenotype (scale bar = 0.5in).


91 Figure 5 3 Screen for polymorphic SSR markers in B73, Mo17, and W22. A) Examples of PCR scores: umc1288 amplifies a single allele; umc1538 has three co dominant alleles; umc1590 and phi402893 have polymorphic alleles that are not suitable for BSA. DN A size markers (bp) are indicated for each image. B/W, M/W, and B/M indicate 1:1 mixes of B73:W22, Mo17:W22, and B73:Mo17 inbred DNA. B) Venn diagram showing the number of co dominant markers found for each pair of inbreds.


92 Figure 5 4 Genetic map of the distributed marker sets. Markers are positioned based on their genetic coordinates on the IBM2 2008 Neighbors genetic map. Gray, open, and black arrowheads are polymorphic markers for the B73/Mo17, B73/W22, and W22/Mo17 inbred pairs, res pectively. The open oval on chromosome 8 indicates the genetic distance added to the map due to misplacement of Emp4. Supplementary table 2 gives map locations and expected co dominant polymorphisms for the distributed marker set.


93 Figure 5 5 Mapping of the rgh3 umu1 seeding genetic modif ier. A) Gel images demonstrate increasing recombination frequency of heterozygous open individuals from umc1170 located at 13.2Mb towards umc1867 found at 5.3Mb Lanes 3 to 8 show individuals showi ng no recombi nation indicating likely phenotyping mis assignments. B) Physical map of the short arm of chromosome 9 showing B73 heretozygous enrichment by multiple SSR markers tested in the area. Markers C9SSR 67, C9SSR 92, and C9SSR 51 showed the highest distortion to wards B73 mapping the modifier locus.


94 Figure 5 6. Fine map of the UniformMu dek locus. A) Recombination frequencies were scored using 42 individual dek/dek individuals from the Mo17/UniformMu F 2 mapping population. Lanes 34 45 are PCR products from severe dek seeds in which maternal pericarp tissue was included in the DNA extraction. Weak amplification of the Mo17 allele was attributed to contaminating parental DNA in these samples. B) Comparison of the predicted genetic distances based on IBM2 2008 Neighbors map coordinates and the observed recombination frequencies relative to the dek locus.


95 Table 5 1. Modified vs. unmodified scoring of BC1 rgh3/rgh3 seedlings Culture Planted Germinated Open high Open low Adherent high Adherent low No Score 08C 0078 11 7 1 0 2 1 3 08C 0079 45 18 1 3 8 1 4 08C 0080 16 10 6 1 1 0 2 08C 0081 19 11 2 1 3 3 2 08C 0082 33 25 7 4 6 3 5 08C 0083 24 13 5 1 3 3 1 Total 148 84 22 10 23 11 17


96 Table 5 2 Number of co dominant markers identified for each inbred pair from 505 SSR markers Total polymorphic markers Distributed marker set Inbred comparison No. of markers Average map interval (cM) S.D. (cM) % Map Covered No. of markers Average map interval (cM) S.D. (cM) % Map Covered B73/Mo17 170 12.0 12.3 91.7 70 26.9 13.2 91.1 B73/W22 161 13.0 11.8 94.6 64 29.1 12.3 90.4 Mo17/W22 154 13.5 11.6 94.5 71 26.6 12.9 92.7 Union of 3 inbred pairs 238 8.9 9.1 95.6 85 22.7 12.0 94.7


97 CHAPTER 6 CONCLUSION S Regulation of RGH3 An ever increasing amount of evidence demonstrates the relevance of alternative splicing as a regulatory mechanism in higher eukaryotes. Even though more is understood about the mechanisms and roles of alternative splicing in vertebrat es and metazoans, research in plants is beginning to demonstrate the biological consequences of alternative splicing. The study of the rgh3 mutant has provided additional understanding regarding the involvement of alternative splicing in the development of endosperm and embryo tissues in maize seeds (Fouquet et al., 2011). The goal of this dissertation is to develop knowledge about the regulation and function of RGH3 in order to understand the mechanisms of alternative splicing in development. The data pres ented here suggests the RGH3 splicing factor is regulated by alternative splicing of its pre mRNA. Regulation through alternative splicing seems to be a common mechanism of control of splicing related genes as demonstrated by multiple studies with SR prote ins and other splicing factors (Iida and Go, 2006; Chung et al., 2007; Lareau et al., 2007a; Palusa et al., 2007; Barta et al., 2008). Thus, alternative splicing of Rgh3 and the observed localization of RGH3 protein isoforms provide additional evidences fo r this type of regulatory mechanism among splicing factors. Moreover, results from quantitative RT PCR analyzes conducted by Fouquet et al. (2011), and western blot analyzes using anti RGH3 antibodies (see Chapter 2, 3, & 4) suggest that regulation of Rgh3 may be influenced in a tissue or developmental manner. Despite these observations, it is not yet clear if the main impacts of Rgh3 splicing take place at the mRNA or protein level. Therefore, additional experiments will


98 be required to test these possibil ities. Additionally even though the presented data does not evidently indicate its participation, regulati on of Rgh3 by the R UST mechanism is still plausible and therefore should also be tested. Furthermore, future work at the protein level should also provide a clearer picture regarding RG H3 regulation and its role in development. RGH3 Splicing and Post Splicing Activities The spliceosome is a very dynamic molecular machine formed by multiple smaller protein RNA complexes (Wahl et al., 2009). In humans, it has been shown that URP protein pa rticipates in both U2 and U12 type spliceosomes (Tronchere et al., 1997; .Shen et al., 2010). Localization of the functional RGH3 protein to nuclear speckles, and its co localization and interaction with U2AF 65 strongly indicates RGH3 participates in the U2 type spliceosome. The aberrant splicing of several genes in the rgh3 umu1 mutant showed a trend for disrupting introns with non canonical dinucleotides suggesting RGH3 also participates in the U12 spliceosome Future experiments to pull down RGH3 protein complexes should provide additional information regarding where and when RGH3 participates in the spliceosome. Identifying additional protein protein interactions with RGH3 should also provide information to explain the localization of RGH3 to the nucleolus. The nucleolus is involved in a wide range of functions from rRNA and RNPs processing, to RNA silencing and post transcriptional mRNA regulation (Brown and Shaw, 2008). In addition, many splicing factors ha ve been implicated in post splicing mechanisms including mRNA nuclear export, NMD, and mRNA translation (Long and Caceres, 2009). The localization of RGH3 to the nucleolus suggests an additional role in post


99 transcriptional activities beyond splicing poten tially including roles in the exon exon junction complex or NMD. rgh3 umu1 Allele Reveals Developmental Roles for RGH3 The rgh3 umu1 allele provides a unique opportunity to study a hypomorphic protein of the URP family. Knockdowns of URP in human cell cult ures are lethal, while the rgh3 umu1 mutant does not affect endosperm cell viab ility in culture (Shen et al., 2010 ; Fouquet et al., 2011). Prior to identifying the rgh3 umu1 allele, it was not feasible to use genetics to study URP orthologs due to the le thal nature of knockout alleles. Through the study of the rgh3 umu1 allele, I was able to investigate RGH3 impacts in alternative splicing demonstrating its involvement in a reduce number of splicing events. Unfortunately, at this stage it is difficult to estimate the number of genes targeted by RGH3, and the low number of genes affected in rgh3 umu1 may not serve as a reference for a whole genome s cale Nevertheless, the data argues that RGH3 is involved in regulation of genes that are likely to have si gnificant impact on the development of the maize seed. The hypomorphic allele also facilitated studies of RGH3 domain functions and will likely allow studies of protein protein interactions in a defective background. From these data and the data presented by Fouquet et al. (2011) regarding the phenotypic impacts of rgh3 umu1 on seed development, it can be argued that RGH3 is involved in the regulation of proteins that are important for proper cell differentiation. Defects in these proteins in turn affect de velopment of the endosperm and influence development of the embryo. Rgh3 has a separate embryo specific function that translates into the observed seedling phenotypes (Fouquet et al., 2011). Finally, through the use of a distributed set of SSR markers, I w as able to place a rgh3 umu1 seedling allele modifier to a 3 Mb interval on the short arm of chromosome 9

PAGE 100

100 (Figure 5 5 ). The mapped interval contains too many genes to discriminate among all of them in search of a candidate gene. In addition the range of rgh3 umu1 seedling phenotypes has hindered the possibilities to fine map a potential gene. Though, by c ombining this map position with results from other experiments th at could uncover RGH3 gene targets or interacting proteins that map within this interval it will be possible to find a candidate gene. These additional experiment may include RNA sequence analyzes, RNA immunoprecipitation analyzes, or protein complexes pull down experiments among others. The nature of the modifier gene is still a matter of sp eculation. However, since the changes in phenotype are observed at the seedling and not at the seed level it could be argued that the modifier gene acts in embryo tissues specifically. Given the variability of the seedling phenotype, and the hypomorphic na ture of RGH3 umu protein, it is also probable that the modifier gene directly interacts with RGH3 either in a protein complex or as a target transcript. Taken together, it can be argued that the seedling modifier is either a splicing factor that interacts with RGH3 or a gene target, such as a transcription factor, that impacts seedling development.

PAGE 101

101 LIST OF REFERENCES Abdalla, K.O., Thomson, J.A., Rafudeen, M.S. (2009). Protocols for nuclei isolation and nuclear protein extraction fro m theresurrection plant Xerophyta viscosa for proteomic studies. Analytic Bioch 384, 365 367 Ahern, K.R., Deewatthanawong, P., Schares, J., Muszynski, M., Weeks, R., Vollbrecht, E., Duvick, J., Brendel, V.P., and Brutnell, T.P. (2009). Regional mutagenesis using Dissociation in maize. Methods 49, 248 254. Ali, G.S., and Reddy, A.S. (2008a). Regulation of alternative splicing of pre mRNAs by stresses. Curr Top Microbiol Immunol 326, 257 275. Ali, G.S., and Reddy, A.S. (2008b). Spatiotemporal organization of pre mRNA splicing proteins in plants. Curr Top Microbiol Immunol 326, 103 118. Ali, G.S., Palusa, S.G., Golovkin, M., Prasad, J., Manley, J.L., and Reddy, A.S. (2007). Regulation of plant developmental processes by a novel splicing factor. PLoS One 2, e471 Appleby, N., Edwards, D., and Batley, J. (2009). New technologies for ultra high throughput genotyping in plants. Methods Mol Biol 513, 19 39. Banerjee, H., Rahn, A., Gawande, B., Guth, S., Valcarcel, J., and Singh, R. (2004). The conserved RNA recognition motif 3 of U2 snRNA auxiliary factor (U2AF 65) is essential in vivo but dispensable for activity in vitro. RNA 10, 240 253. Barbaglia, A.M., Klusman, K.M., Higgins, J., Shaw, J.R., Hannah, L.C., and Lal, S.K. (2012). Gene cap ture by Helitron transposons reshuffles the transcriptome of maize. Genetics 190, 965 975. (2008). Plant SR proteins and their functions. Curr Top Microbiol Immunol 326, 83 102. Bennetzen, J.L. (2000). Transposable element contributions to plant gene and genome evolution. Plant Mol Biol 42, 251 269. Black, D.L. (2003). Mechanisms of alternative pre messenger RNA splicing. Annu Rev Biochem 72, 291 336. Bortiri, E., Jackson, D., and Hake, S. (2006). Advances in maize genomics: the emergence of positional cloning. Curr Opin Plant Biol 9, 164 171. Brown, J.W., and Shaw, P.J. (2008). The role of the plant nucleolus in pre mRNA processing. Curr Top Microbiol Immunol 326, 291 311. Brutnell, T.P. (2002). Transposon tagging i n maize. Funct Integr Genomics 2, 4 12.

PAGE 102

102 Carson, M.L., Stuber, C.W., and Senior, M.L. (2004). Identification and Mapping of Quantitative Trait Loci Conditioning Resistance to Southern Leaf Blight of Maize Caused by Cochliobolus heterostrophus Race O. Phytop athology 94, 862 867. Chang M T Neu ff er M G (1994) Endosperm embryo interaction in maize. Maydica 39 9 18 Chang, Y.F., Imam, J.S., and Wilkinson, M.F. (2007). The nonsense mediated decay RNA surveillance pathway. Annu Rev Biochem 76, 51 74. Chen, M., and Manley, J.L. (2009). Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol 10, 741 754. Cho, S., Hoang, A., Sinha, R., Zhong, X.Y., Fu, X.D., Krainer, A.R., and Ghosh, G. (2011). Interact ion between the RNA binding domains of Ser Arg splicing factor 1 and U1 70K snRNP protein determines early spliceosome assembly. Proc Natl Acad Sci U S A 108, 8233 8238. Citovsky, V., Lee, L.Y., Vyas, S., Glick, E., Chen, M.H., Vainstein, A., Gafni, Y., Ge lvin, S.B., and Tzfira, T. (2006). Subcellular localization of interacting proteins by bimolecular fluorescence complementation in planta. J Mol Biol 362, 1120 1131. Cowperthwaite, M., Park, W., Xu, Z., Yan, X., Maurais, S.C., and Dooner, H.K. (2002). Use of the transposon Ac as a gene searching engine in the maize genome. Plant Cell 14, 713 726. Diao, X.M., and Lisch, D. (2006a). Mutator transposon in maize and MULEs in the plant genome. Yi Chuan Xue Bao 33, 477 487. Docquier, S., Tillemans, V., Deltour, R ., and Motte, P. (2004). Nuclear bodies and compartmentalization of pre mRNA splicing factors in higher plants. Chromosoma 112, 255 266. Domon, D., Lorkovic, Z.J.,Valcarcel, J., and Filipowicz, W. (1998). Multiple Forms of the U2 Small Nuclear Ribonucleopr otein Auxiliary Factor U2AF Subunits Expressed in Higher Plants J Bio Chem. 273, 34603 34610 Dowhan, D.H., Hong, E.P., Auboeuf, D., Dennis, A.P., Wilson, M.M., Berget, S.M., and O'Malley, B.W. (2005). Steroid hormone receptor coactivation and alternative RNA splicing by U2AF65 related proteins CAPERalpha and CAPERbeta. Mol Cell 17, 429 439. Fang, Y., Hearn, S., and Spector, D.L. (2004). Tissue specific expression and dynamic organization of SR splicing factors in Arabidopsis. Mol Biol Cell 15, 2664 2673. Fajardo, D. (2008). Putative Role for RNA Splicing in Maize Endosperm Embryo

PAGE 103

103 Developmental Interactions is Revealed by the rough endosperm 3 ( rgh3 ) Seed Mutant. PhD Dissertation. University of Florida, Gainesville, Florida. Fernandes, J., Dong, Q., Schneider, B., Morrow, D.J., Nan, G.L., Brendel, V., and Walbot, V. (2004). Genome wide mutagenesis of Zea mays L. using RescueMu transposons. Genome Biol 5, R82. Feschotte, C., Jiang, N., and Wessler, S.R. (2002). Plant transposable elements: where geneti cs meets genomics. Nat Rev Genet 3, 329 341. Filichkin, S.A., Priest, H.D., Givan, S.A., Shen, R., Bryant, D.W., Fox, S.E., Wong, W.K., and Mockler, T.C. (2010). Genome wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 20, 45 58. Fou quet, R., Martin, F., Fajardo, D.S., Gault, C.M., Gmez, E., Tseung, C.W., Policht, T., Hueros, G., and Settles, A.M. (2011). Maize rough endosperm3 encodes an RNA splicing factor required for endosperm cell differentiation and has a nonautonomous effect o n embryo development. Plant Cell 23, 4280 4297. Frilander, M.J., and Steitz, J.A. (1999). Initial recognition of U12 dependent introns requires both U11/5' splice site and U12/branchpoint interactions. Genes Dev 13, 851 863. Fu, Y., Wen, T.J., Ronin, Y.I., Chen, H.D., Guo, L., Mester, D.I., Yang, Y., Lee, M., Korol, A.B., Ashlock, D.A., and Schnable, P.S. (2006). Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize. Genetics 174, 1671 1683. Gallavotti, A., Barazesh, S., Malcomber, S., Hall, D., Jackson, D., Schmidt, R.J., and McSteen, P. (2008). sparse inflorescence1 encodes a monocot specific YUCCA like gene required for vegetative and reproductive development in maize. Proc Natl Acad Sci U S A 105, 15196 15201. Girard, L., and Freeling, M. (1999). Regulatory changes as a consequence of transposon insertion. Dev Genet 25, 291 296. Golovkin, M., and Reddy, A.S. (1998). The plant U1 small nuclear ribonucleoprotein particle 70K protein interacts with two novel serine/argini ne rich proteins. Plant Cell 10, 1637 1648. Gutirrez Marcos, J.F., Dal Pr, M., Giulini, A., Costa, L.M., Gavazzi, G., Cordelier, S., Sellam, O., Tatout, C., Paul, W., Perez, P., Dickinson, H.G., and Consonni, G. (2007). empty pericarp4 encodes a mitochondrion targeted pentatricopeptide repeat protein necessary for seed development and plant growth in maize. Plant Cell 19, 196 210. Haldane, J.B.S. (1919) The combination o f linkage values and the calcu lation of distance between the loci of linked factors. J Genet 8 299 309

PAGE 104

104 Hamblin, M.T., Warburton, M.L., and Buckler, E.S. (2007). Empirical comparison of Simple Sequence Repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness. PLoS One 2, e136 7. Hastings, M.L., Allemand, E., Duelli, D.M., Myers, M.P., and Krainer, A.R. (2007). Control of pre mRNA splicing by the general splicing factors PUF60 and U2AF(65). PLoS One 2, e538. Heckel, T., Werner, K., Sheridan, W.F., Dumas, C., and Rogowsky, P.M. ( 1999). Novel phenotypes and developmental arrest in early embryo specific mutants of maize. Planta 210, 1 8. Horton, R.M., Hunt, H.D., Ho, S.N., Pullen, J.K., and Pease, L.R. (1989). Engineering hybrid genes without the use of restriction enzymes: gene spl icing by overlap extension. Gene 77, 61 68. Hua Van, A., Le Rouzic, A., Maisonhaute, C., and Capy, P. (2005). Abundance, distribution and dynamics of retrotransposable elements and transposons: similarities and differences. Cytogenet Genome Res 110, 426 44 0. Iida, K., and Go, M. (2006). Survey of conserved alternative splicing events of mRNAs encoding SR proteins in land plants. Mol Biol Evol 23, 1085 1094. Isshiki, M., Tsumoto, A., and Shimamoto, K. (2006). The serine/arginine rich protein family in rice p lays important roles in constitutive and alternative splicing of pre mRNA. Plant Cell 18, 146 158. Jander, G., Norris, S.R., Rounsley, S.D., Bush, D.F., Levin, I.M., and Last, R.L. (2002). Arabidopsis map based cloning in the post genome era. Plant Physiol 129, 440 450. Jones, E.S., Sullivan, H., Bhattramakki, D., and Smith, J.S. (2007). A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize (Zea mays L.). Theor Appl Genet 115, 361 371. Kalyna, M., Lopato, S., and Barta, A. (2003). Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development. Mol Biol Cell 14, 3565 3577. Kalyna, M., Simpson, C.G., Syed, N.H., Lewandowska, D., Marque z, Y., Kusenda, B., Marshall, J., Fuller, J., Cardle, L., McNicol, J., Dinh, H.Q., Barta, A., and Brown, J.W. (2012). Alternative splicing and nonsense mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res 40, 2 454 2469. Karimi, M., Inz, D., and Depicker, A. (2002). GATEWAY vectors for Agrobacterium mediated plant transformation. Trends Plant Sci 7, 193 195.

PAGE 105

105 Karimi, M., Depicker, A., and Hilson, P. (2007). Recombinational cloning with plant gateway vectors. Plant Physiol 145, 1144 1154. Keren, H., Lev Maor, G., and Ast, G. (2010). Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet 11, 345 355. Kidwell, M.G, Lisch, D. (1997). Transposable elements as sources of v a riation in animals and plants. Proc. Natl. Acad. Sci. U.S. A 94 7704 7711 Kielkopf, C.L., Lcke, S., and Green, M.R. (2004). U2AF homology motifs: protein recognition in the RRM world. Genes Dev 18, 1513 1526. Kielkopf, C.L., Rodionova, N.A., Green, M.R., and Burley, S.K. (2001). A novel peptide recognition mode revealed by the X ray structure of a core U2AF35/U2AF65 heterodimer. Cell 106, 595 605. Kim, S.H., Koroleva, O.A., Lewandowska, D., Pendle, A.F., Clark, G.P., Simpson, C.G., Shaw, P.J., and Brown, J.W. (2009). Aberrant mRNA transcripts and the nonsense mediated decay proteins UPF2 and UPF3 are enriched in the Arabidopsis nucleolus. Plant Cell 21, 2045 2057. Kitagawa, K., Wang, X., Hatada, I., Yamaoka, T., Nojima, H., Inazawa, J., Abe, T., Mitsuya, K ., Oshimura, M., and Murata, A. (1995). Isolation and mapping of human homologues of an imprinted mouse gene U2af1 rs1. Genomics 30, 257 263. Kolkman, J.M., Conrad, L.J., Farmer, P.R., Hardeman, K., Ahern, K.R., Lewis, P.E., Sawers, R.J., Lebejko, S., Chom et, P., and Brutnell, T.P. (2005). Distribution of Activator (Ac) throughout the maize genome for use in regional mutagenesis. Genetics 169, 981 995. Koroleva, O.A., Calder, G., Pendle, A.F., Kim, S.H., Lewandowska, D., Simpson, C.G., Jones, I.M., Brown, J .W., and Shaw, P.J. (2009). Dynamic behavior of Arabidopsis eIF4A III, putative core protein of exon junction complex: fast relocation to nucleolus and splicing speckles under hypoxia. Plant Cell 21, 1592 1606. Lamond, A.I., and Spector, D.L. (2003). Nucle ar speckles: a model for nuclear organelles. Nat Rev Mol Cell Biol 4, 605 612. Lareau, L.F., Brooks, A.N., Soergel, D.A., Meng, Q., and Brenner, S.E. (2007a). The coupling of alternative splicing and nonsense mediated mRNA decay. Adv Exp Med Biol 623, 190 211. Lareau, L.F., Inada, M., Green, R.E., Wengrod, J.C., and Brenner, S.E. (2007b). Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446, 926 929.

PAGE 106

106 Lee, M., Sharopova, N., Beavis, W.D., Grant, D., K att, M., Blair, D., and Hallauer, A. (2002). Expanding the genetic map of maize with the intermated B73 x Mo17 (IBM) population. Plant Mol Biol 48, 453 461. Lewis, B.P., Green, R.E., and Brenner, S.E. (2003). Evidence for the widespread coupling of alternative splicing and nonsense mediated mRNA decay in humans. Proc Natl Acad Sci U S A 100, 189 192. Lisch, D. (2002). Mutator transposons. Trends Plant Sci 7, 498 504. Liu, S., Chen, H.D., Makarevitch, I., Shirmer, R., Emrich, S.J., Dietrich, C.R., Barbazuk, W.B., Springer, N.M., and Schnable, P.S. (2010). High throughput genetic mapping of mutants via quantitative single nucleotide polymorphism typing. Genetics 184, 19 26. Long, J.C., and Caceres, J.F. (2009). The SR protein family of splicing facto rs: master regulators of gene expression. Biochem J 417, 15 27. Lopato, S., Kalyna, M., Dorner, S., Kobayashi, R., Krainer, A.R., and Barta, A. (1999). atSRp30, one of two SF2/ASF like proteins from Arabidopsis thaliana, regulates splicing of specific plan t genes. Genes Dev 13, 987 1001. Lopes, M.A., Takasaki, K., Bostwick, D.E., Helentjaris, T., and Larkins, B.A. (1995). Identification of two opaque2 modifier loci in quality protein maize. Mol Gen Genet 247, 603 613. Lorkovic, Z.J., Lehner, R., Forstner, C ., and Barta, A. (2005). Evolutionary conservation of minor U12 type spliceosome between plants and humans. RNA 11, 1095 1107. (2004). Use of fluorescent protein tags to study nuclear organization of the spliceos omal machinery in transiently transformed living plant cells. Mol Biol Cell 15, 3233 3243. (2008). Co localisation studies of Arabidopsis SR splicing factors reveal different types of speckles in plant cell nucle i. Exp Cell Res 314, 3175 3186. Lu, T., Lu, G., Fan, D., Zhu, C., Li, W., Zhao, Q., Feng, Q., Zhao, Y., Guo, Y., Huang, X., and Han, B. (2010). Function annotation of the rice transcriptome at single nucleotide resolution by RNA seq. Genome Res 20, 1238 12 49. Marquez, Y., Brown, J.W., Simpson, C., Barta, A., and Kalyna, M. (2012). Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res 22, 1184 1195. Matlin, A.J., Clark, F., and Smith, C.W. (2005). Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 6, 386 398.

PAGE 107

107 Matsuoka, Y., Vigouroux, Y., Goodman, M.M., Sanchez G, J., Buckler, E., and Doebley, J. (2002). A single domestication for maize shown by multilocus microsatelli te genotyping. Proc Natl Acad Sci U S A 99, 6080 6084. May, B.P., Liu, H., Vollbrecht, E., Senior, L., Rabinowicz, P.D., Roh, D., Pan, X., Stein, L., Freeling, M., Alexander, D., and Martienssen, R. (2003). Maize targeted mutagenesis: A knockout resource f or maize. Proc Natl Acad Sci U S A 100, 11541 11546. McCarty, D.R., Settles, A.M., Suzuki, M., Tan, B.C., Latshaw, S., Porch, T., Robin, K., Baier, J., Avigne, W., Lai, J., Messing, J., Koch, K.E., and Hannah, L.C. (2005). Steady state transposon mutagenes is in inbred maize. Plant J 44, 52 61. McGlincy, N.J., and Smith, C.W. (2008). Alternative splicing resulting in nonsense mediated mRNA decay: what is the meaning of nonsense? Trends Biochem Sci 33, 385 393. Mollet, I., Barbosa Morais, N.L., Andrade, J., a nd Carmo Fonseca, M. (2006). Diversity of human U2AF splicing factors. FEBS J 273, 4807 4816. Moore, M.J., and Sharp, P.A. (1993). Evidence for two active sites in the spliceosome provided by stereochemistry of pre mRNA splicing. Nature 365, 364 368. Neu ff er M G England D (1995) Induced mutations with confirmed locations. Maize Genetics Coop News Lett 69:43 46 Neuffer, M.G., Coe, E.H., and Wessler, S.R. (1997). Mutants of Maize. (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press ) Nilsen, T.W. and Graveley, B.R. (2010). Expansion of the eukaryotic proteome by alternative splicing. Nature 463, 457 463. Ortiz, D.F., and Strommer, J.N. (1990). The Mu1 maize transposable element induces tissue specific aberrant splicing and polyadenylation in two Adh1 mutants. Mol Cell Biol 10, 2090 2095. Palusa, S.G., and Reddy, A.S. (2010). Extensive coupling of alternative splicing of pre mRNAs of serine/arginine (SR) genes with nonsense mediated decay. New Phytol 185, 83 89. Palusa, S.G., Ali, G.S., and Reddy, A.S. (2007). Alternative splicing of pre mRNAs of Arabidopsis serine/arginine rich proteins: regulation by hormones and stresses. Plant J 49, 1091 1107. Patel, A.A., and Steitz, J.A. (2003). Splicing double: insights from the second spliceosome. Nat Rev Mo l Cell Biol 4, 960 970.

PAGE 108

108 Pendle, A.F., Clark, G.P., Boon, R., Lewandowska, D., Lam, Y.W., Andersen, J., Mann, M., Lamond, A.I., Brown, J.W., and Shaw, P.J. (2005). Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. Mol Biol Cell 16, 260 269. Pribat, A., Noiriel, A., Morse, A.M., Davis, J.M., Fouquet, R., Loizeau, K., Ravanel, S., Frank, W., Haas, R., Reski, R., Bedair, M., Sumner, L.W., and Hanson, A.D. (2010). Nonflowering plants possess a unique folate dependent phenylalani ne hydroxylase that is localized in chloroplasts. Plant Cell 22, 3410 3422. Proost, S., Van Bel, M., Sterck, L., Billiau, K., Van Parys, T., Van de Peer, Y., and Vandepoele, K. (2009). PLAZA: a comparative genomics resource to study gene and genome evoluti on in plants. Plant Cell 21, 3718 3731. Purugganan, M., and Wessler, S. (1992). The splicing of transposable elements and its role in intron evolution. Genetica 86, 295 303. Quesada, V., Macknight, R., Dean, C., and Simpson, G.G. (2003). Autoregulation of FCA pre mRNA processing controls Arabidopsis flowering time. EMBO J 22, 3142 3152. Reddy, A.S.N. ( 2001 ) Nuclear pre mRNA splicing in plants. Crit. Rev. Plant Sci. 20 523 71 Reddy, A.S. (2007). Alternative splicing of pre messenger RNAs in plants in the genomic era. Annu Rev Plant Biol 58, 267 294. Reddy, A.S., Day, I.S., Ghring, J., and Barta, A. (2012). Localization and dynamics of nuclear speckles in plants. Plant Physiol 158, 67 77. Reid, K.E., Olsson, N., Schlosser, J., Peng, F., a nd Lund, S.T. (2006). An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real time RT PCR during berry development. BMC Plant Biol 6, 27. Scanlon, M.J., Stinard, P.S., James, M.G., Myers, A.M., and Robertson D.S. (1994). Genetic analysis of 63 mutations affecting maize kernel development isolated from Mutator stocks. Genetics 136, 281 294. Selenko, P., Gregorovic, G., Sprangers, R., Stier, G., Rhani, Z., Krmer, A., and Sattler, M. (2003). Structural basis f or the molecular recognition between human splicing factors U2AF65 and SF1/mBBP. Mol Cell 11, 965 976. Settles, A.M., Latshaw, S., and McCarty, D.R. (2004). Molecular analysis of high copy insertion sites in maize. Nucleic Acids Res 32, e54.

PAGE 109

109 Settles, A.M., Holding, D.R., Tan, B.C., Latshaw, S.P., Liu, J., Suzuki, M., Li, L., O'Brien, B.A., Fajardo, D.S., Wroclawska, E., Tseung, C.W., Lai, J., Hunter, C.T., Avigne, W.T., Baier, J., Messing, J., Hannah, L.C., Koch, K.E., Becraft, P.W., Larkins, B.A., and McCa rty, D.R. (2007). Sequence indexed mutations in maize using the UniformMu transposon tagging population. BMC Genomics 8, 116. Settles, A.M. (2009) Transposon tagging and reverse genetics. In: Kriz A, Larkens B (eds) Molecular genetic approaches to maize i mprovement. Springer, Berlin, pp 143 160 Sharopova, N., McMullen, M.D., Schultz, L., Schroeder, S., Sanchez Villeda, H., Gardiner, J., Bergstrom, D., Houchins, K., Melia Hancock, S., Musket, T., Duru, N., Polacco, M., Edwards, K., Ruff, T., Register, J.C., Brouwer, C., Thompson, R., Velasco, R., Chin, E., Lee, M., Woodman Clikeman, W., Long, M.J., Liscum, E., Cone, K., Davis, G., and Coe, E.H. (2002). Development and mapping of SSR markers for maize. Plant Mol Biol 48, 463 481. Shav Tal, Y., Blechman, J., Darzacq, X., Montagna, C., Dye, B.T., Patton, J.G., Singer, R.H., and Zipori, D. (2005). Dynamic sorting of nuclear components into distinct nucleolar caps during transcriptional inhibition. Mol Biol Cell 16, 2395 2413. Shen, H., Zheng, X., Luecke, S., and Green, M.R. (2010). The U2AF35 related protein Urp contacts the 3' splice site to promote U12 type intron splicing and the second step of U2 type intron splicing. Genes Dev 24, 2389 2394. Slotkin, R.K., and Martienssen, R. (2007). Transposable elements an d the epigenetic regulation of the genome. Nat Rev Genet 8, 272 285. Spector, D.L., and Lamond, A.I. (2011). Nuclear speckles. Cold Spring Harb Perspect Biol 3 Stauffer, E., Westermann, A., Wagner, G., and Wachter, A. (2010). Polypyrimidine tract binding protein homologues from Arabidopsis underlie regulatory circuits based on alternative splicing and downstream control. Plant J 64, 243 255. Tanabe, N., Yoshimura, K., Kimura, A., Yabuta, Y., and Shigeoka, S. (2007). Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, atSR30 and atSR45a, in response to environmental stress. Plant Cell Physiol 48, 1036 1049. Tavanez, J.P., Madl, T., Kooshapur, H., Sattler, M., and Valcrcel, J. (2012). hnRNP A1 proofreads 3' splice site recognition by U2AF. Mol Cell 45, 314 329.

PAGE 110

110 Thompson, B.E., Bartling, L., Whipple, C., Hall, D.H., Sakai, H., Schmidt, R., and Hake, S. (2009). bearded ear encodes a MADS box transcription factor critical for maize floral development. Plant Cell 21, 2578 25 90. Till, B.J., Reynolds, S.H., Weil, C., Springer, N., Burtner, C., Young, K., Bowers, E., Codomo, C.A., Enns, L.C., Odden, A.R., Greene, E.A., Comai, L., and Henikoff, S. (2004). Discovery of induced point mutations in maize genes by TILLING. BMC Plant B iol 4, 12. Tillemans, V., Dispa, L., Remacle, C., Collinge, M., and Motte, P. (2005). Functional distribution and dynamics of Arabidopsis SR splicing factors in living plant cells. Plant J 41, 567 582. Tillemans, V., Leponce, I., Rausin, G., Dispa, L., and Motte, P. (2006). Insights into nuclear organization in plants as revealed by the dynamic distribution of Arabidopsis SR splicing factors. Plant Cell 18, 3218 3234. Tronchre, H., Wang, J., and Fu, X.D. (1997). A protein related to splicing factor U2AF35 that interacts with U2AF65 and SR proteins in splicing of pre mRNA. Nature 388, 397 400. Tzfira, T., Tian, G.W., Lacroix, B., Vyas, S., Li, J., Leitner Dagan, Y., Krichevsky, A., Taylor, T., Vainstein, A., and Citovsky, V. (2005). pSAT vectors: a modular s eries of plasmids for autofluorescent protein tagging and expression of multiple genes in plants. Plant Mol Biol 57, 503 516. Vollbrecht, E., Reiser, L., and Hake, S. (2000). Shoot meristem size is dependent on inbred background and presence of the maize h omeobox gene, knotted1. Development 127, 3161 3172. Wahl, M.C., Will, C.L., and Lhrmann, R. (2009). The spliceosome: design principles of a dynamic RNP machine. Cell 136, 701 718. Wang, B.B., and Brendel, V. (2004). The ASRG database: identification and s urvey of Arabidopsis thaliana genes involved in pre mRNA splicing. Genome Biol 5, R102. Wang, B.B., and Brendel, V. (2006a). Molecular characterization and phylogeny of U2AF35 homologs in plants. Plant Physiol 140, 624 636. Wang, B.B., and Brendel, V. (200 6b). Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci U S A 103, 7175 7180. Wang, E.T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S.F., Schroth, G.P., and Burge, C.B. (2008). Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470 476.

PAGE 111

111 Well C.F., Wessler, S.R (1990). The effects of plant transposable element inserfion on transcription initiation and RNA processing. Annu Rev Plant Physiol Plant Mol Biol 41, 527 552 Wessler, S.R., Bureau, T.E., and White, S.E. (1995). LTR retrotransposons and MITEs: important players in the evolution of plant genomes. Curr Opin Genet Dev 5, 814 821. Will, C.L., Schneider, C., Hossbach, M., Urlaub, H., Rauhut, R., Elbashir, S., Tuschl, T., and Lhrmann, R. (2004). The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2 dependent spliceosome. RNA 10, 929 941. Wise, A.A., Liu, Z., and Binns, A.N. (2006). Three methods for the introduction of foreign DNA into Agrob acterium. Methods Mol Biol 343, 43 53. Wu, S., Romfo, C.M., Nilsen, T.W., and Green, M.R. (1999). Functional recognition of the 3' splice site AG by the splicing factor U2AF35. Nature 402, 832 835. Xing, Y., and Lee, C. (2006). Alternative splicing and RNA selection pressure -evolutionary consequences for eukaryotic genomes. Nat Rev Genet 7, 499 509. Zamore, P.D., Patton, J.G., and Green, M.R. (1992). Cloning and domain structure of the mammalian splicing factor U2AF. Nature 355, 609 614. Zhang, X.N., and M ount, S.M. (2009). Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development. Plant Physiol 150, 1450 1458.

PAGE 112

112 BIOGRAPHICAL SKETCH Federico Martin was born in Santa Fe, Argentina. He graduated from El Portal high school in December 1999. He then moved to Tempe, Arizona to become part of s swimming varsity team at Ari zona State University where he began his undergraduate studies in January 2001. While an undergraduate student, Federico worked as a research assistant in the Shool of Life Sciences under the supervision of Dr. Willem Vermaas studying hydrogen photoproduction in the cyanobacteria Shynechocystis sp pcc 6803. He then switched laboratories to wor k as a research assistant in the Center for Infectious Diseases and Vaccinology under the supervision of Dr. Guy Cardineau. The research topic was plant based vaccine production methods Federico graduated in May 2005 with a Bachelors of Science degree in molecular biosciences and b iotechnology. After his graduation, he continued working as a accepted in the Plant Molecular and Cellular Biology (PMCB) program at the University of Florida. In January 2007, he initiated his Ph.D project under the supervision of Dr. A. Mark Settles studying the function of the ROUGH ENDOSPERM3 (RGH3) protein in the model system Zea mays.