XAP5 CIRCADIAN TIMEKEEPER regulates RNA splicing and the circadian clock via genetically separable pathways

The circadian oscillator allows organisms to synchronize their cellular and physiological activities with diurnal environmental changes. In plants, the circadian clock is primarily composed of multiple transcriptional-translational feedback loops. Regulators of post-transcriptional events, such as pre-mRNA splicing factors, are also involved in controlling the pace of the clock. However, in most cases the underlying mechanisms remain unclear. We have previously identified XAP5 CIRCADIAN TIMEKEEPER (XCT) as an Arabidopsis thaliana circadian clock regulator with uncharacterized molecular functions. Here, we report that XCT physically interacts with components of the spliceosome, including members of the Nineteen Complex (NTC). PacBio Iso-Seq data show that xct mutants have transcriptome-wide pre-mRNA splicing defects, predominantly aberrant 3’ splice site selection. Expression of a genomic copy of XCT fully rescues those splicing defects, demonstrating that functional XCT is important for splicing. Dawn-expressed genes are significantly enriched among those aberrantly spliced in xct mutants, suggesting that the splicing activity of XCT may be circadian regulated. Furthermore, we show that loss of function mutations in PRP19A or PRP19B, two homologous core NTC components, suppress the short circadian period phenotype of xct-2. Interestingly, we do not see rescue of the splicing defects of core clock genes in prp19 xct mutants. Similarly, we find that transgenic expression of the fission yeast ortholog of XCT in Arabidopsis shortens the circadian period without affecting splicing. Taken together, our results suggest that XCT may regulate splicing and the clock function through genetically separable pathways. One sentence summary XCT plays genetically separable roles in controlling the fidelity of 3’ splice site selection during pre-mRNA splicing and the pace of circadian clock in Arabidopsis