PAPS1-associated alternative polyadenylation changes correlate with pollen development and flowering time in Arabidopsis

Alternative polyadenylation (APA) serves as a critical co-transcriptional regulatory mechanism that shapes mRNA fate and protein function. POLY(A) POLYMERASE 1 (PAPS1) contributes to poly(A) tail synthesis; however, its relationship to poly(A) site choice is less well characterized. Here, we profiled PAPS1-associated poly(A) site usage across Arabidopsis (Arabidopsis thaliana) tissues using UMI-quantified poly(A) tag sequencing (qPAT-seq). Across tissues, paps1-4 showed tissue-dependent shifts in poly(A) site usage, with pronounced effects in pollen. In the paps1-4 mutant, polyadenylated transcripts were biased toward longer isoforms with significantly longer 3' UTRs, and poly(A) signal usage was altered in distinct ways: a U-to-A shift immediately downstream of poly(A) sites occurred in leaves and flower buds, whereas pollen showed more complex motif combinations with reduced usage of canonical cis-elements. In pollen, DE-APAGs included multiple genes previously linked to a pollen developmental regulatory module involving AT-RICH INTERACTING DOMAIN-CONTAINING PROTEIN 1 (ARID1), RETINOBLASTOMA RELATED 1 (RBR1), and DUO POLLEN1 (DUO1), showing coordinated changes in APA and expression. Flowering-time-related terms were also enriched among genes with significantly altered APA in paps1-4, including regulators connected to FLOWERING LOCUS C (FLC) and photoperiod responses, and these changes were more consistent with poly(A) site selection differences than with widespread poly(A) tail length changes. Notably, multiple poly(A) factors in pollen switched between single- and multi-poly(A) site usage patterns in paps1-4, representing a major component of PAPS1-associated regulation. Together, these findings reveal tissue-specific APA alterations associated with PAPS1 and highlight pollen and flowering pathways as key contexts of its regulatory influence.