Loss of splicing factor SR45 reshapes tissue-dependent alternative polyadenylation landscapes and transcriptome responses to salt in Arabidopsis

Serine/arginine-rich 45 (SR45) is a plant-specific SR-like splicing factor and an RNA-binding protein involved in Arabidopsis development and stress responses. Although SR45 has been primarily studied for its role in pre-mRNA alternative splicing (AS), whether it also regulates alternative polyadenylation (APA) remains unclear. Here, we combined poly(A) tag sequencing (PAT-seq) and RNA-seq to examine APA, AS, and gene expression in wild-type (WT) and sr45-1 plants across inflorescence, leaf, and root under normal conditions, and in leaf and root under prolonged mild salinity. Under normal conditions, SR45 loss caused widespread changes in poly(A) site usage, with distal site shifts occurring more frequently than proximal shifts across tissues. APA, AS, and differential gene expression showed only partial overlap, with significant enrichment between APA and AS but not with gene expression changes, indicating that APA represents a distinct layer of SR45-mediated transcriptome regulation. Under prolonged mild salinity conditions, pairwise analyses showed preference of distal poly(A) site usage in WT and proximal site usage in sr45-1, particularly in leaf. Replicate-aware genotype-by-treatment interaction analyses further identified genotype-dependent differences in APA and gene expression, where more genotype-treatment interacting genes detected in leaf than in root. Genes encoding polyadenylation and splicing factors also showed changes in APA, AS, or transcript abundance. Together, these results expand the known role of SR45 from splicing regulation to APA-associated transcriptome remodeling and reveal that SR45 is required for proper salt-responsive changes in transcript abundance in Arabidopsis.