Maize<i>Rough Endosperm3</i>Encodes an RNA Splicing Factor Required for Endosperm Cell Differentiation and Has a Nonautonomous Effect on Embryo Development

Fouquet, Romain; Martin, Federico; Fajardo, Diego; Gault, Christine M.; Gómez, Elisa; Tseung, Chi-Wah; Policht, Tyler; Hueros, Gregorio; Settles, A. Mark

doi:10.1105/tpc.111.092163

Cited by 56 publications

(93 citation statements)

References 87 publications

(96 reference statements)

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“…The RGH3 protein localizes to the nucleolus and to speckles in the nucleoplasm and colocalizes with U2AF 65 . The rgh3 mutant did not have a general splicing defect but affected AS of some transcripts and appeared to induce the use of noncanonical splice sites (Fouquet et al, 2011). SUPPRESSOR OF abi3-5 (SUA) is a novel SF in Arabidopsis that affects seed maturation by controlling AS of ABSCISIC ACID INSENSITIVE3 (ABI3).…”

Section: Function Of Sfs In Developmentmentioning

confidence: 99%

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

2013

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High-throughput sequencing for transcript profiling in plants has revealed that alternative splicing (AS) affects a much higher proportion of the transcriptome than was previously assumed. AS is involved in most plant processes and is particularly prevalent in plants exposed to environmental stress. The identification of mutations in predicted splicing factors and spliceosomal proteins that affect cell fate, the circadian clock, plant defense, and tolerance/sensitivity to abiotic stress all point to a fundamental role of splicing/AS in plant growth, development, and responses to external cues. Splicing factors affect the AS of multiple downstream target genes, thereby transferring signals to alter gene expression via splicing factor/AS networks. The last two to three years have seen an ever-increasing number of examples of functional AS. At a time when the identification of AS in individual genes and at a global level is exploding, this review aims to bring together such examples to illustrate the extent and importance of AS, which are not always obvious from individual publications. It also aims to ensure that plant scientists are aware that AS is likely to occur in the genes that they study and that dynamic changes in AS and its consequences need to be considered routinely.

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Section: Function Of Sfs In Developmentmentioning

confidence: 99%

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

2013

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“…5E). Another U2AF splicing factor, ROUGH ENDOSPERM3, has been implicated in seed development (Fouquet et al, 2011), while GRMZM5G813627 may instead play a role in tassel.…”

Section: Seed Embryo and Endosperm Undergo Hundreds Of Developmentamentioning

confidence: 99%

“…Tissuespecific splicing patterns can also alter a transcript's sensitivity to regulation by microRNAs, such as the maize (Zea mays) SPX family, which produces miR827-sensitive isoforms that predominate in developing seedlings, while insensitive isoforms dominate other tissues (Thatcher et al, 2014). Gene expression changes in splicing factors also play key roles in guiding tissuespecific developmental processes, including seed development, where the U2AF splicing factor ROUGH ENDOSPERM3 has been shown to be involved in mediating the interaction between the embryo and endosperm (Fouquet et al, 2011). The control of these alternative splicing differences among different tissues is thought to be the result of differential splicing factor expression and is likely also influenced by tissue-specific methylation patterns (Regulski et al, 2013).…”

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confidence: 99%

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

et al. 2015

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Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage-or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition.After transcription, the majority of eukaryotic premRNA is subjected to a series of posttranscriptional modifications, including the removal of introns to form a mature mRNA (Stamm et al., 2005). Although some introns are removed constitutively, many can be processed in a variety of alternative ways, including exon skipping, intron retention, alternative acceptor, alternative donor, and alternative position (change in both acceptor and donor positions; Lorkovic et al., 2000). These alternative splicing events form a crucial regulatory level and have the ability to alter an mRNA's stability, localization, and protein products. Alternative splicing events are controlled by a variety of cis-elements, including the presence of consensus splice sequences at the intron-exon border and intronic and exonic splicing enhancer sequences (Pertea et al., 2007). Trans-acting factors also exert a strong effect on splicing and are mostly composed of Ser/Arg-rich proteins, which typically promote intron removal, and heterogenous nuclear ribonucleoproteins, which typically inhibit it (Erkelenz et al., 2013). A host of other indirect factors can affect splicing, including transcription rate, methylation status, and any cellular conditions that alter RNA secondary structure (Kornblihtt et al

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“…Verification will come from genome-wide studies of AS in different organs and during development (Loraine et al, 2013) as has been shown in animals Kalsotra and Cooper, 2011;BarbosaMorais et al, 2012;Ellis et al, 2012). In addition, screens for mutants in various pathways have frequently identified splicing factors as modulators of functional proteins, indicating that these pathways are regulated via differential splicing (Lee et al, 2006;Monaghan et al, 2009;Sugliani et al, 2010;Fouquet et al, 2011;Koncz et al, 2012). There is an ever-growing body of literature on how alternative splicing (AS) influences important developmental and signaling pathways, and many important examples have been discussed in the accompanying review by Staiger and Brown (2013).…”

Section: Introductionmentioning

confidence: 99%

Complexity of the Alternative Splicing Landscape in Plants

et al. 2013

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Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.

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MaizeRough Endosperm3Encodes an RNA Splicing Factor Required for Endosperm Cell Differentiation and Has a Nonautonomous Effect on Embryo Development

Cited by 56 publications

References 87 publications

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

Complexity of the Alternative Splicing Landscape in Plants

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