SCR106 splicing factor modulates abiotic stress responses by maintaining the RNA splicing in rice.

Plants employ sophisticated molecular machinery to fine-tune their responses to growth, developmental, and stress cues. Gene expression influences the plant's cellular responses through regulatory processes like transcription and splicing. Pre-mRNA is alternatively spliced to increase the genome coding potential and further regulate the expression. Serine/Arginine-rich (SR) proteins, a family of pre-mRNA splicing factors, recognize splicing cis-elements and regulate both constitutive and alternative splicing. Several studies reported SR protein genes in the rice genome, subdivided into six subfamilies based on their domain structures. Here, we identified a new splicing factor in rice with RNA recognition motif (RRM) and SR-dipeptides and is related to the SR proteins, subfamily SC. OsSCR106 regulates pre-mRNA splicing under abiotic stress conditions. OsSCR106 localizes to the nuclear speckles, a major site for pre-mRNA splicing in the cell. Loss-of-function scr106 mutant is hypersensitive to salt, ABA, and low-temperature stress and harbors developmental abnormality indicated by the shorter length of shoot and root. The hypersensitivity to stress phenotypes was rescued by complementation using OsSCR106 fused behind its endogenous promoter. Global gene expression and genome-wide splicing analysis in wild-type and scr106 seedlings revealed that OsSCR106 regulates its targets, presumably through regulating the alternative 3´ splice site. Under salt stress conditions, we identified multiple splice isoforms regulated by OsSCR106. Collectively, our results suggest OsSCR106 is an important splicing factor that plays a crucial role in accurate pre-mRNA splicing and regulates abiotic stress responses in plants.