One Gene, Many Proteins: Mapping Cell-Specific Alternative Splicing in Plants

Swarup, Ranjan; Crespi, Martín; Bennett, Malcolm J.

doi:10.1016/j.devcel.2016.11.002

Cited by 17 publications

(15 citation statements)

References 10 publications

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“…Other processes also condition the transcriptional response. Alternative splicing mechanisms are known to create novel regulatory opportunities that influence transcript behavior in different tissues, stages and the response upon environmental changes [50]. In fact, putative alternative splicing forms of the rice SUMOylation machinery have been identified but remained unexplored [51].…”

Section: Introductionmentioning

confidence: 99%

Insights into the transcriptional and post-transcriptional regulation of the rice SUMOylation machinery and into the role of two rice SUMO proteases

et al. 2018

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BackgroundSUMOylation is an essential eukaryotic post-translation modification that, in plants, regulates numerous cellular processes, ranging from seed development to stress response. Using rice as a model crop plant, we searched for potential regulatory points that may influence the activity of the rice SUMOylation machinery genes.ResultsWe analyzed the presence of putative cis-acting regulatory elements (CREs) within the promoter regions of the rice SUMOylation machinery genes and found CREs related to different cellular processes, including hormone signaling. We confirmed that the transcript levels of genes involved in target-SUMOylation, containing ABA- and GA-related CREs, are responsive to treatments with these hormones. Transcriptional analysis in Nipponbare (spp. japonica) and LC-93-4 (spp. indica), showed that the transcript levels of all studied genes are maintained in the two subspecies, under normal growth. OsSUMO3 is an exceptional case since it is expressed at low levels or is not detectable at all in LC-93-4 roots and shoots, respectively. We revealed post-transcriptional regulation by alternative splicing (AS) for all genes studied, except for SUMO coding genes, OsSIZ2, OsOTS3, and OsELS2. Some AS forms have the potential to alter protein domains and catalytic centers. We also performed the molecular and phenotypic characterization of T-DNA insertion lines of some of the genes under study. Knockouts of OsFUG1 and OsELS1 showed increased SUMOylation levels and non-overlapping phenotypes. The fug1 line showed a dwarf phenotype, and significant defects in fertility, seed weight, and panicle architecture, while the els1 line showed early flowering and decreased plant height. We suggest that OsELS1 is an ortholog of AtEsd4, which was also supported by our phylogenetic analysis.ConclusionsOverall, we provide a comprehensive analysis of the rice SUMOylation machinery and discuss possible effects of the regulation of these genes at the transcriptional and post-transcriptional level. We also contribute to the characterization of two rice SUMO proteases, OsELS1 and OsFUG1.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1547-3) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Insights into the transcriptional and post-transcriptional regulation of the rice SUMOylation machinery and into the role of two rice SUMO proteases

et al. 2018

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“…AS diversifies transcriptome and expands protein coding capacity, having a profound impact on protein functionality, stability and expression levels [12,13,14,15]. In plants, 40%–63% of AS frequencies have been reported for the expressed multi-exon genes [16,17,18,19,20,21,22].…”

Section: Introductionmentioning

confidence: 99%

Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato

Wang

Weng

et al. 2017

IJMS

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Phenotypic plasticity is the phenomenon that one particular genotype produces different phenotypes under different environmental conditions, but its underlying molecular and genetic mechanisms are poorly understood. Plastic traits may be under the control of genes whose expression is modulated by environmental cues. In this study, we investigated phenotypic plasticity in tomato (Solanum lycopersicum) and its ancestral species S. pimpinellifolium by comparing the global gene expression of young seedlings grown under two distinct growth conditions. Our results show that more than 7000 genes exhibited differential expression in response to environmental changes from phytotron to a plastic greenhouse, and 98 environmentally sensitive genes displayed the same patterns of expression response across the two tomato species. We also found that growth conditions had a remarkable impact on transcriptome complexity, attributable to alternative splicing (AS), in which 665 splice variants showed differential expression in response to the environmental changes. Moreover, more splice variants and AS events per gene were detected in plastic greenhouse-grown seedlings than their phytotron counterparts, and these seedlings also had higher percentages of intron retention events. The identification of the conserved environmentally-sensitive genes and the splice variants in this study will be useful for further analysis of gene regulation of environmental response in tomato and other crops.

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“…This result is consistent with previous reports in nervous system and brain 33 , 52 . Recent studies have demonstrated that AS not only can increase proteome diversity, but also regulate gene expression 14 , 53 . Therefore, the tissue-specific AS events obtained in this study will provide a strong basis in further investigation of the effects of AS on proteome diversity and gene expression.…”

Section: Discussionmentioning

confidence: 99%

Landscape of alternative splicing in Capra_hircus

Feng

et al. 2018

Sci Rep

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Alternative splicing (AS) is a fundamental regulatory process in all higher eukaryotes. However, AS landscapes for a number of animals, including goats, have not been explored to date. Here, we sequenced 60 samples representing 5 tissues from 4 developmental stages in triplicate using RNA-seq to elucidate the goat AS landscape. In total, 14,521 genes underwent AS (AS genes), accounting for 85.53% of intron-containing genes (16,697). Among these AS genes, 6,342 were differentially expressed in different tissues. Of the AS events identified, retained introns were most prevalent (37.04% of total AS events). Functional enrichment analysis of differential and specific AS genes indicated goat AS mainly involved in organ function and development. Particularly, AS genes identified in leg muscle were associated with the “regulation of skeletal muscle tissue development” GO term. Given genes were associated with this term, four of which (NRG4, IP6K3, AMPD1, and DYSF) might play crucial roles in skeletal muscle development. Further investigation indicated these five genes, harbored 13 ASs, spliced exclusively in leg muscle, likely played a role in goat leg muscle development. These results provide novel insights into goat AS landscapes and a valuable resource for investigation of goat transcriptome complexity and gene regulation.

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One Gene, Many Proteins: Mapping Cell-Specific Alternative Splicing in Plants

Cited by 17 publications

References 10 publications

Insights into the transcriptional and post-transcriptional regulation of the rice SUMOylation machinery and into the role of two rice SUMO proteases

Insights into the transcriptional and post-transcriptional regulation of the rice SUMOylation machinery and into the role of two rice SUMO proteases

Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato

Landscape of alternative splicing in Capra_hircus

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