Alternative splicing in plants – coming of age

Syed, Naeem H.; Kalyna, Maria; Márquez, Yamile; Barta, Andrea; Brown, John W.

doi:10.1016/j.tplants.2012.06.001

Cited by 419 publications

(387 citation statements)

References 103 publications

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“…Linked AS-NMD thus regulates the level of functional mRNA transcripts (which encode protein) via targeted degradation of alternative splice forms (McGlincy and Smith, 2008;Nicholson and Mühlemann, 2010), and in Arabidopsis thaliana, at least 13% of genes undergo AS-NMD . The second main consequence of AS is where transcript isoforms give rise to proteins that differ in their sequence and domain arrangement and thus may widely differ in subcellular localization, stability, or function (Syed et al, 2012). Proteins or polypeptides that are truncated as a consequence of AS can act as dominant-negative inhibitors of the authentic proteins (e.g., through unproductive interaction with dimerization partners or nucleic acids) and have been designated micropeptides or small interfering peptides .…”

Section: Introductionmentioning

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: Introductionmentioning

confidence: 99%

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

2013

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“…Besides its fundamental role in constitutive gene expression, pre-mRNA processing also increases transcriptome complexity by producing distinct mRNA variants from one type of pre-mRNA, thereby providing an additional layer of gene regulation. In particular, alternative pre-mRNA splicing (AS) and alternative 39 end processing have been found to expand transcriptome diversity enormously in both animals (Mangone et al, 2010;Nilsen and Graveley, 2010) and plants (Reddy, 2007;Hunt, 2011;Syed et al, 2012). While alternative 39 end processing generates mRNAs of variable lengths, an even more diverse outcome can be achieved by AS via removal of variable single or multiple intronic regions.…”

Section: Introductionmentioning

confidence: 99%

Polypyrimidine Tract Binding Protein Homologs from Arabidopsis Are Key Regulators of Alternative Splicing with Implications in Fundamental Developmental Processes

et al. 2012

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Alternative splicing (AS) generates transcript variants by variable exon/intron definition and massively expands transcriptome diversity. Changes in AS patterns have been found to be linked to manifold biological processes, yet fundamental aspects, such as the regulation of AS and its functional implications, largely remain to be addressed. In this work, widespread AS regulation by Arabidopsis thaliana Polypyrimidine tract binding protein homologs (PTBs) was revealed. In total, 452 AS events derived from 307 distinct genes were found to be responsive to the levels of the splicing factors PTB1 and PTB2, which predominantly triggered splicing of regulated introns, inclusion of cassette exons, and usage of upstream 59 splice sites. By contrast, no major AS regulatory function of the distantly related PTB3 was found. Dependent on their position within the mRNA, PTB-regulated events can both modify the untranslated regions and give rise to alternative protein products. We find that PTB-mediated AS events are connected to diverse biological processes, and the functional implications of selected instances were further elucidated. Specifically, PTB misexpression changes AS of PHYTOCHROME INTERACTING FACTOR6, coinciding with altered rates of abscisic acid-dependent seed germination. Furthermore, AS patterns as well as the expression of key flowering regulators were massively changed in a PTB1/2 level-dependent manner.

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“…These factors bind to cis elements on the pre-mRNA to promote or inhibit the recruitment of spliceosome components to the adjacent alternative splice sites (19). Therefore, the regulation of AS depends on the expression level and posttranslational modification of SR proteins and other splicing factors (20). It has been reported that light affects the AS of several genes in plants (16)(17)(18).…”

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confidence: 99%

Phytochrome controls alternative splicing to mediate light responses in Arabidopsis

Shikata

Hanada

Ushijima

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

157

174

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Plants monitor the ambient light conditions using several informational photoreceptors, including red/far-red light absorbing phytochrome. Phytochrome is widely believed to regulate the transcription of light-responsive genes by modulating the activity of several transcription factors. Here we provide evidence that phytochrome significantly changes alternative splicing (AS) profiles at the genomic level in Arabidopsis, to approximately the same degree as it affects steady-state transcript levels. mRNA sequencing analysis revealed that 1,505 and 1,678 genes underwent changes in their AS and steady-state transcript level profiles, respectively, within 1 h of red light exposure in a phytochromedependent manner. Furthermore, we show that splicing factor genes were the main early targets of AS control by phytochrome, whereas transcription factor genes were the primary direct targets of phytochrome-mediated transcriptional regulation. We experimentally validated phytochrome-induced changes in the AS of genes that are involved in RNA splicing, phytochrome signaling, the circadian clock, and photosynthesis. Moreover, we show that phytochrome-induced AS changes of SPA1-RELATED 3, the negative regulator of light signaling, physiologically contributed to promoting photomorphogenesis. Finally, photophysiological experiments demonstrated that phytochrome transduces the signal from its photosensory domain to induce light-dependent AS alterations in the nucleus. Taking these data together, we show that phytochrome directly induces AS cascades in parallel with transcriptional cascades to mediate light responses in Arabidopsis.phytochrome | alternative splicing | light signaling | posttranscriptional regulation | photomorphogenesis

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Alternative splicing in plants – coming of age

Cited by 419 publications

References 103 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

Polypyrimidine Tract Binding Protein Homologs from Arabidopsis Are Key Regulators of Alternative Splicing with Implications in Fundamental Developmental Processes

Phytochrome controls alternative splicing to mediate light responses in Arabidopsis

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