Transcriptome Analyses of FY Mutants Reveal Its Role in mRNA Alternative Polyadenylation

Abstract

A crucial step for mRNA polyadenylation is poly(A) signal recognition by <i>trans</i>-acting factors. The mammalian cleavage and polyadenylation specificity factor (CPSF) complex components CPSF30 and WD repeat-containing protein33 (WDR33) recognize the canonical AAUAAA for polyadenylation. In Arabidopsis (<i>Arabidopsis thaliana</i>), the flowering time regulator FY is the homolog of WDR33. However, its role in mRNA polyadenylation is poorly understood. Using poly(A) tag sequencing, we found that >50% of alternative polyadenylation (APA) events are altered in <i>fy</i> single mutants or double mutants with <i>oxt6</i> (a null mutant of <i>AtCPSF30</i>), but mutation of the FY WD40-repeat has a stronger effect than deletion of the plant-unique Pro-Pro-Leu-Pro-Pro (PPLPP) domain. <i>fy</i> mutations disrupt AAUAAA or AAUAAA-like poly(A) signal recognition. Notably, A-rich signal usage is suppressed in the WD40-repeat mutation but promoted in PPLPP-domain deficiency. However, <i>fy</i> mutations do not aggravate the altered signal usage in <i>oxt6</i> Furthermore, the WD40-repeat mutation shows a preference for 3' untranslated region shortening, but the PPLPP-domain deficiency shows a preference for lengthening. Interestingly, the WD40-repeat mutant exhibits shortened primary roots and late flowering with alteration of APA of related genes. Importantly, the long transcripts of two APA genes affected in <i>fy</i> are related to abiotic stress responses. These results reveal a conserved and specific role of FY in mRNA polyadenylation.