Depletion of Arabidopsis SC35 and SC35-like serine/arginine-rich proteins affects the transcription and splicing of a subset of genes

Yan, Qingqing; Xia, Xi; Sun, Zhenfei; Fang, Yuda

doi:10.1371/journal.pgen.1006663

Cited by 88 publications

(103 citation statements)

References 127 publications

Supporting

Mentioning

101

Contrasting

Order By: Relevance

“…While a quintuple mutant in SC35 and SCL genes displays pleiotropic alterations in plant morphology and development, no phenotypic changes were observed for the other mutants, including the sr quadruple mutant that is supposedly defective in the expression of the related factors SR34, SR34a, SR34b, and SR30. However, our analysis of the T-DNA insertion line SALK_116747C in SR30, which was used by Yan et al (2017), revealed no difference in the SR30 expression pattern compared to the wild type (Supplemental Fig. S3A), suggesting that the sr quadruple mutant generated by Yan et al (2017) is, at least for SR30, not a knockout.…”

Section: Fine-tuning Sr30 Expression Via As In Development and Stressmentioning

confidence: 87%

“…However, our analysis of the T-DNA insertion line SALK_116747C in SR30, which was used by Yan et al (2017), revealed no difference in the SR30 expression pattern compared to the wild type (Supplemental Fig. S3A), suggesting that the sr quadruple mutant generated by Yan et al (2017) is, at least for SR30, not a knockout. Besides analyzing full knockout mutants, it will be of interest to examine phenotypes of sr mutants under specific growth conditions including stress regimes.…”

Section: Fine-tuning Sr30 Expression Via As In Development and Stressmentioning

confidence: 87%

“…Furthermore, evidence for SR30-mediated AS regulation of its homolog SR34 and other genes has been previously provided, based on changes in their splicing patterns in the SR30 overexpression lines (Lopato et al, 1999). A recent study aiming at elucidating the physiological functions of SR proteins generated multiple mutants for all subfamilies of SR proteins (Yan et al, 2017). While a quintuple mutant in SC35 and SCL genes displays pleiotropic alterations in plant morphology and development, no phenotypic changes were observed for the other mutants, including the sr quadruple mutant that is supposedly defective in the expression of the related factors SR34, SR34a, SR34b, and SR30.…”

Section: Fine-tuning Sr30 Expression Via As In Development and Stressmentioning

confidence: 99%

See 2 more Smart Citations

Subcellular Compartmentation of Alternatively Spliced Transcripts Defines SERINE/ARGININE-RICH PROTEIN30 Expression

2018

View full text Add to dashboard Cite

Alternative splicing (AS) is prevalent in higher eukaryotes, and generation of different AS variants is tightly regulated. Widespread AS occurs in response to altered light conditions and plays a critical role in seedling photomorphogenesis, but despite its frequency and effect on plant development, the functional role of AS remains unknown for most splicing variants. Here, we characterized the light-dependent AS variants of the gene encoding the splicing regulator Ser/Arg-rich protein SR30 in Arabidopsis (Arabidopsis thaliana). We demonstrated that the splicing variant SR30.2, which is predominantly produced in darkness, is enriched within the nucleus and strongly depleted from ribosomes. Light-induced AS from a downstream 39 splice site gives rise to SR30.1, which is exported to the cytosol and translated, coinciding with SR30 protein accumulation upon seedling illumination. Constitutive expression of SR30.1 and SR30.2 fused to fluorescent proteins revealed their identical subcellular localization in the nucleoplasm and nuclear speckles. Furthermore, expression of either variant shifted splicing of a genomic SR30 reporter toward SR30.2, suggesting that an autoregulatory feedback loop affects SR30 splicing. We provide evidence that SR30.2 can be further spliced and, unlike SR30.2, the resulting cassette exon variant SR30.3 is sensitive to nonsense-mediated decay. Our work delivers insight into the complex and compartmentalized RNA processing mechanisms that control the expression of the splicing regulator SR30 in a light-dependent manner.Maturation of eukaryotic mRNAs involves intricate co-and posttranscriptional RNA processing, which has critical functions in regulating gene expression and diversifying the transcriptome. Among several mechanisms, alternative precursor mRNA splicing (AS) in particular generates many transcript variants by removing distinct intronic regions and joining the resulting exons. Deep analysis of transcriptomes via high-throughput RNA sequencing (RNA-seq) has revealed that a major fraction of all intron-containing genes from higher eukaryotes generates AS variants. In humans, more than 95% of multiexon genes display AS (Pan et al., 2008). The prevalence of AS has also been demonstrated for other eukaryotes including plants (Reddy et al., 2013;Staiger and Brown, 2013), with current estimates of ;61% and ;42% of intron-containing genes giving rise to AS variants in the model plants Arabidopsis (Arabidopsis thaliana;Marquez et al., 2012) and Brachypodium distachyon (Mandadi and Scholthof, 2015), respectively.Besides its pivotal role in increasing the coding and regulatory capacity of the transcriptome, AS finetunes gene expression by varying the output ratios of splicing variants. The full extent of AS regulation likely exceeds the current estimates, as the production of many transcript variants can be specifically controlled under certain conditions, such as cell and tissue types, developmental stages, and in response to stresses and other environmental factors (Reddy et al., 2013;Staige...

show abstract

Section: Fine-tuning Sr30 Expression Via As In Development and Stressmentioning

confidence: 87%

Section: Fine-tuning Sr30 Expression Via As In Development and Stressmentioning

confidence: 87%

Section: Fine-tuning Sr30 Expression Via As In Development and Stressmentioning

confidence: 99%

See 1 more Smart Citation

Subcellular Compartmentation of Alternatively Spliced Transcripts Defines SERINE/ARGININE-RICH PROTEIN30 Expression

2018

View full text Add to dashboard Cite

show abstract

“…Having confirmed the utility of SpliSER, we also implemented a method that would allow detection of differentially spliced sites across the genome between samples. To assess the efficacy of this approach, we applied SpliSER on a previously published RNA-Seq data on quintuple mutants of the sc35-scl in Arabidopsis thaliana 25 . In this comparison, Yan et al, utilised ASD to detect 213 differentially spliced events representing 199 genes (p-value<0.05) of which 34 were detected after FDR based analysis (FDR<0.05) 25 .…”

Section: Resultsmentioning

confidence: 99%

“…An alternative approach evolved from a historical description of various types of splicing events such as intron retention, exon skipping, mutually exclusive exons and 5' and 3' alternative splice sites etc 22,23 . Several approaches including rMATS 24 , ASD 25 , SUPPA2 26 rely on quantifying splicing events. However, grouping splicing events across different genes to make inferences (e.g., increase in exon skipping or intron retention in a mutant compared to wild type) suggests biological categorization and common regulatory mechanism, which can be misleading.…”

Section: Introductionmentioning

confidence: 99%

Splice-site Strength Estimation: A simple yet powerful approach to analyse RNA splicing

Dent¹,

Singh²,

Mishra

et al. 2020

Preprint

View full text Add to dashboard Cite

Association Studies.RNA splicing, and variations in this process referred to as alternative splicing, are critical aspects of gene regulation in eukaryotes. From environmental responses in plants to being a primary link between genetic variation and disease in humans, splicing differences confer extensive phenotypic changes across diverse organisms 1-3 . Current approaches for analysing splicing rely on quantifying variant transcripts (i.e., isoforms) or splicing events (i.e., intron retention, exon skipping etc) 4,5 . However, regulation of splicing occurs at the level of selection of individual splice sites, which results in variation in the abundance of isoforms and/or splicing events. Here, we present a simple approach to quantify the strength of individual splice sites, which determines their selection in a splicing reaction.Splice-site strength, as a quantitative phenotype, allows us to analyse splicing precisely in unprecedented ways. We demonstrate the power of this approach in defining the genomic determinants of the strength of individual splice-sites through GWAS. Our pilot-GWAS with more than thousand splice sites hints that cis-sequence divergence and competition between splice-sites and are among the primary determinants of variation in splicing among natural accessions of Arabidopsis thaliana. This approach allows deciphering the principles of splicing, which in turn has implications that range from agriculture to medicine.

show abstract

Defense strategies against sweet potato chlorotic stunt and pakakuy virus coinfection unraveled

Kiemo,

Salamon,

Tóth

et al. 2024

Crop Science

View full text Add to dashboard Cite

This study into the response of two Ipomoea batatas (L.) Lam cultivars, Melinda and Tio Joe, to coinfection with sweet potato chlorotic stunt virus (SPCSV) and sweet potato pakakuy virus (SPPV), employed a comprehensive approach encompassing symptomatology, real‐time quantitative polymerase chain reaction, metagenomics, and transcriptomics. SPCSV is a quarantine virus with synergistic effects, which decimate yields. SPPV is the most prevalent DNA virus in sweet potato germplasm, with a tendency to persist in meristems, posing a significant risk for germplasm transfer between territories. Graft inoculation experiments revealed that while Tio Joe remained asymptomatic for 12 weeks and suppressed virus replication, Melinda displayed symptoms early on and exhibited high virus titers. Metagenomic analyses corroborated these observations and confirmed that SPCSV and SPPV were responsible. Transcriptomic analysis unveiled disparities in gene expression between Melinda and Tio Joe. Differential gene expression was heightened and altered in Melinda as the viruses disrupted its gene expression. Its defense strategies, such as inducing abscisic acid signaling, were insufficient to overcome disruptive viral effects like oxidative stress, rendering it susceptible. In contrast, Tio Joe had relatively stable differential gene expression, indicating resistance to SPPV–SPCSV coinfection. Overexpressed genes such as sirtuin, rapid alkalization factor, and nuclear pore anchor triggered quantitative resistance, supported with enriched organelles such as mitochondrion and pathways such as proteasome and cutin, suberine, and wax biosynthesis. Tio Joe maintained its genome integrity and inhibited viral replication by tightly controlling gene expression and preventing reactive oxygen species accumulation.

show abstract

Depletion of Arabidopsis SC35 and SC35-like serine/arginine-rich proteins affects the transcription and splicing of a subset of genes

Cited by 88 publications

References 127 publications

Subcellular Compartmentation of Alternatively Spliced Transcripts Defines SERINE/ARGININE-RICH PROTEIN30 Expression

Subcellular Compartmentation of Alternatively Spliced Transcripts Defines SERINE/ARGININE-RICH PROTEIN30 Expression

Splice-site Strength Estimation: A simple yet powerful approach to analyse RNA splicing

Defense strategies against sweet potato chlorotic stunt and pakakuy virus coinfection unraveled

Contact Info

Product

Resources

About