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

Abstract

AbstractThe 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 identifiedXAP5 CIRCADIAN TIMEKEEPER(XCT) as anArabidopsis thalianacircadian 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 thatxctmutants have transcriptome-wide pre-mRNA splicing defects, predominantly aberrant 3’ splice site selection. Expression of a genomic copy ofXCTfully rescues those splicing defects, demonstrating that functionalXCTis important for splicing. Dawn-expressed genes are significantly enriched among those aberrantly spliced inxctmutants, suggesting that the splicing activity ofXCTmay be circadian regulated. Furthermore, we show that loss of function mutations inPRP19AorPRP19B, two homologous core NTC components, suppress the short circadian period phenotype ofxct-2. However, we do not see rescue of the splicing defects of core clock genes inprp19 xctmutants. Therefore, our results suggest thatXCTmay regulate splicing and the clock function through genetically separable pathways.