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

Abstract

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...

Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome

“…The TF genes included a high proportion of circadian clock genes as well as genes associated with abiotic stress, flowering time, and hormone responses (Supplemental Data Sets 12 and 13). The SF-RBP genes included serinearginine-rich (SR) and heterogeneous ribonucleoprotein particle (hnRNP) protein genes such as SR30, RBM25, and GEMIN2 known to be involved in stress responses and/or regulation of the clock (Reddy et al, 2013;Schlaen et al, 2015;Cheng et al, 2017;Hartmann et al, 2018) (see Discussion). For many of the early AS genes, the AS changes were either only observed in day 1 at 4°C or persisted through the cold treatment, and many involved isoform switches (Supplemental Data Set 12).…”

Brassica Rapa SR45a Regulates Drought Tolerance via the Alternative Splicing of Target Genes

“…Nonetheless, the determination of the SR45a target genes and their splicing patterns under particular stress conditions will provide vital clues as to their functional role in stress responses, which have yet to be identified. SR proteins participate in multiple signaling pathways, including the glucose signaling pathway [18], the nonsense-mediated mRNA decay pathway (NMD), which is involved in the RNA surveillance system [19], the ABA signaling pathway [20], the autonomous flowering pathway [21], and stress response gene expression pathways. There is mounting evidence implicating AtSR genes in the signal transduction of the abscisic acid (ABA) phytohormone, a key modulator of various abiotic stress responses (drought, high salinity, light, cold, and heat) in plants [5,22].…”

The U1 snRNP Subunit LUC7 Modulates Plant Development and Stress Responses via Regulation of Alternative Splicing

“…Error bars denote se of the mean. nucleus and not in the cytosol (Göhring et al, 2014;Hartmann et al, 2018). In addition, in metazoans, intron retention might have a more general role in regulating gene expression (Yap et al, 2012;Braunschweig et al, 2014;Pimentel et al, 2016;Naro et al, 2017).…”