Perspective on Alternative Splicing and Proteome Complexity in Plants

Chaudhary, Saurabh; Jabre, Ibtissam; Reddy, Anireddy S. N.; Staiger, Dorothee; Syed, Naeem H.

doi:10.1016/j.tplants.2019.02.006

Cited by 109 publications

(98 citation statements)

References 108 publications

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“…This shift involves translational control (Juntawong et al , ) and the sequestration and/or degradation of many mRNA species via cytoplasmic organelles (Chantarachot and Bailey‐Serres, ) (P‐bodies and stress bodies, for example). The combination of post‐transcriptional and translation controls serves to effectively and rapidly reprogramme protein biosynthesis in response to stress (Chaudhary et al , ).…”

Section: Discussionmentioning

confidence: 99%

Wide‐ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum

et al. 2020

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Alternative polyadenylation (APA) regulates diverse developmental and physiological processes through its effects on gene expression, mRNA stability, translatability, and transport. Sorghum is a major cereal crop in the world and, despite its importance, not much is known about the role of post-transcriptional regulation in mediating responses to abiotic stresses in Sorghum. A genome-wide APA analysis unveiled widespread occurrence of APA in Sorghum in response to drought, heat, and salt stress. Abiotic stress treatments incited changes in poly(A) site choice in a large number of genes. Interestingly, abiotic stresses led to the re-directing of transcriptional output into non-productive pathways defined by the class of poly(A) site utilized. This result revealed APA to be part of a larger global response of Sorghum to abiotic stresses that involves the re-direction of transcriptional output into non-productive transcriptional and translational pathways. Large numbers of stress-inducible poly(A) sites could not be linked with known, annotated genes, suggestive of the existence of numerous unidentified genes whose expression is strongly regulated by abiotic stresses. Furthermore, we uncovered a novel stress-specific cis-element in intronic poly(A) sites used in drought-and heat-stressed plants that might play an important role in non-canonical poly(A) site choice in response to abiotic stresses.

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Section: Discussionmentioning

confidence: 99%

Wide‐ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum

et al. 2020

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“…On the other hand, some proteomic studies suggest that AS may not significantly contribute to protein diversity and only single dominant isoforms are represented at the protein level for most of the protein-coding genes (Ezkurdia et al, 2015; Tress et al, 2017a). Apparently, these contradictions stem from the lower depth and limitations of mass spectrometry (MS) techniques to detect changes in protein domains as a result of AS (Wang et al, 2018; Chaudhary et al, 2019). In this review, basic differences in the mechanism of AS and its contribution toward protein diversity in plants and humans are discussed.…”

Section: Introductionmentioning

confidence: 99%

Alternative Splicing and Protein Diversity: Plants Versus Animals

et al. 2019

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Plants, unlike animals, exhibit a very high degree of plasticity in their growth and development and employ diverse strategies to cope with the variations during diurnal cycles and stressful conditions. Plants and animals, despite their remarkable morphological and physiological differences, share many basic cellular processes and regulatory mechanisms. Alternative splicing (AS) is one such gene regulatory mechanism that modulates gene expression in multiple ways. It is now well established that AS is prevalent in all multicellular eukaryotes including plants and humans. Emerging evidence indicates that in plants, as in animals, transcription and splicing are coupled. Here, we reviewed recent evidence in support of co-transcriptional splicing in plants and highlighted similarities and differences between plants and humans. An unsettled question in the field of AS is the extent to which splice isoforms contribute to protein diversity. To take a critical look at this question, we presented a comprehensive summary of the current status of research in this area in both plants and humans, discussed limitations with the currently used approaches and suggested improvements to current methods and alternative approaches. We end with a discussion on the potential role of epigenetic modifications and chromatin state in splicing memory in plants primed with stresses.

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“…The choice of splice sites mainly depends on the recruitment of splicing factors and heterogeneous nuclear ribonucleoproteins (hnRNPs), but other splicing regulators such as SR proteins and KH-domain RBPs are also involved in this process (8,9). In addition to transcripts encoding proteins with different properties, AS leads to the production of transcripts with a premature termination codon (PTC) that marks them for degradation by the nonsense-medicated decay (NMD) mechanism (10)(11)(12). In Arabidopsis, 61% of genes including the components of the circadian oscillator such as morning-phased CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), day-phased PSEUDO-RESPONSE REGULATORs (PRRs) and REVEILLE 8 (RVE8), evening-phased TIMING OF CAB EXPRESSION 1 (TOC1), GIGANTEA (GI), EARLY FLOWERING 3 (ELF3) have been shown to be alternatively spliced (13)(14)(15)(16).…”

Section: Introductionmentioning

confidence: 99%

The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation

Yang

Sancar

et al. 2020

Journal of Biological Chemistry

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The circadian clock in plants temporally coordinates biological processes throughout the day, synchronizing gene expression with diurnal environmental changes. Circadian oscillator proteins are known to regulate the expression of clock-controlled plant genes by controlling their transcription. Here, using a high-throughput RNA-Seq approach, we examined genome-wide circadian and diurnal control of the Arabidopsis transcriptome, finding that the oscillation patterns of different transcripts of multitranscript genes can exhibit substantial differences and demonstrating that the circadian clock affects posttranscriptional regulation. In parallel, we found that two major posttranscriptional mechanisms, alternative splicing (AS; especially intron retention) and alternative polyadenylation (APA), display circadian rhythmicity resulting from oscillation in the genes involved in AS and APA. Moreover, AS-related genes exhibited rhythmic AS and APA regulation, adding another layer of complexity to circadian regulation of gene expression. We conclude that the Arabidopsis circadian clock not only controls transcription of genes but also affects their posttranscriptional regulation by influencing alternative splicing and alternative polyadenylation.

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Perspective on Alternative Splicing and Proteome Complexity in Plants

Cited by 109 publications

References 108 publications

Wide‐ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum

Wide‐ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum

Alternative Splicing and Protein Diversity: Plants Versus Animals

The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation

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