Subcellular Compartmentation of Alternatively Spliced Transcripts Defines <i>SERINE/ARGININE-RICH PROTEIN30</i> 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 (<i>Arabidopsis thaliana</i>). We demonstrated that the splicing variant <i>SR30.2</i>, which is predominantly produced in darkness, is enriched within the nucleus and strongly depleted from ribosomes. Light-induced AS from a downstream 3' splice site gives rise to <i>SR30.1</i>, 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 <i>SR30</i> reporter toward <i>SR30.2</i>, suggesting that an autoregulatory feedback loop affects <i>SR30</i> splicing. We provide evidence that <i>SR30.2</i> can be further spliced and, unlike <i>SR30.2</i>, the resulting cassette exon variant <i>SR30.3</i> 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.