Regulation of pre-mRNA splicing by light signal in Arabidopsis thaliana

Light signal regulates plant growth and development by controlling a plethora of gene expression changes. Post-transcriptional regulation, especially pre-mRNA processing, is a key step in controlling gene expression; however, the molecular mechanisms linking pre-mRNA processing and light signaling are not well understood. Here we have identified a small functional group of splicing factors, including SFPS (Splicing Factor for Phytochrome Signaling), RRC1 (Reduced Red-light Responses in cry1cry2 Background 1), and SWAP (Suppressor-of-White-Apricot Domain Containing Protein). Genetic studies have shown that sfps and rrc1 single mutants displayed similar long hypocotyl and early flowering phenotype. The double mutant phenotype is similar to sfps single, further confirming that these two proteins function similarly while regulating diverse light responses. Mechanistic studies revealed these two proteins directly interact with each other both in vitro and in vivo. SFPS, reported as the U2 spliceosome-associated splicing factors in animal systems, has also been found to co-localize with U2 spliceosome components (such as U2AF65B, U2AF35A, and U2A’) and RRC1 in the nucleoplasm and nuclear speckles in Arabidopsis. To identify the targets bound by these RNA binding proteins, we sequenced the dark grown sfps and rrc1 mutants irradiated with or without 3hrs of red light. The results indicate SFPS and RRC1 regulate thousands of genes expression through affecting the pre-mRNA splicing in the transcriptome. The splicing defective genes are significantly enriched in “red light stimulus”, “circadian clock” and “photoperiodism”, which further explained the photomorphogenesis and flowering time phenotypes of the sfps and rrc1 mutants. At the same time, two subsets of the co-regulated genes have been identified in dark and light conditions, respectively, revealing the collaborative roles of these two proteins in regulating pre-mRNA splicing. Finally, red light photoreceptor phyB has been discovered to directly interact with SFPS in a red light dependent manner. pifq mutant can completely restore the light hyposensitive phenotype of sfps. All the evidence linked the upstream light signaling pathway to the pre-mRNA splicing mechanisms in plants. However, the molecular mechanisms by which phytochromes modulate the activities of the splicing machineries are still unknown. Taken together, these data suggest that SFPS and RRC1 form a splicing complex functioning downstream of phytochromes, and fine-tune various light responses through regulating pre-mRNA splicingPlant Biolog