XAP5 CIRCADIAN TIMEKEEPER coordinates circadian rhythms and anthocyanin biosynthesis independently of splicing.

Circadian clocks provide plants with an adaptive advantage by enabling them to anticipate daily environmental changes. The periodicity of circadian clocks is regulated at multiple levels of gene expression, including transcription, mRNA processing, translation, and protein modification. Numerous mRNA splicing factors have been implicated in maintaining circadian period length. However, these factors often play additional roles in transcription, making it difficult to determine whether they affect the clock through splicing-dependent or splicing-independent mechanisms. We and others have shown that XAP5 CIRCADIAN TIMEKEEPER (XCT) and components of the PRE-MRNA-PROCESSING FACTOR 19 (PRP19) complex, including the functionally redundant PRP19A and PRP19B, physically associate and regulate both splicing and circadian rhythms. Here, our transcriptome analyses reveal that the antagonistic regulation of circadian period length by XCT and PRP19 likely occurs through splicing-independent mechanisms. Interestingly, both factors co-regulate expression of a substantial set of shared target genes involved in RNA metabolism, photosynthesis, and stress responses despite having largely distinct targets for splicing. Gene co-expression analysis followed by functional characterization identified anthocyanin biosynthesis as another process antagonistically regulated by XCT and PRP19. Nonetheless, we found genetic perturbation of anthocyanin production does not affect circadian period, suggesting that the observed correlation between anthocyanin levels and circadian period may instead reflect disruption of a shared upstream regulatory pathway. Together, our findings suggest involvement of XCT and PRP19 in the transcriptional coordination of anthocyanin biosynthesis and biological timing, expanding their known roles beyond mRNA splicing.