Identification of specific transcripts for plant heat stress tolerance through genome-wide analysis of SIZ1-dependent alternative polyadenylation

Heat stress (HS) has emerged as a significant environmental factor affecting plant growth and agricultural productivity. Alternative polyadenylation (APA) is a crucial co-transcriptional process that regulates developmental processes and stress responses in plants. However, the distinct roles of its resultant transcripts in plant HS response remain to be investigated. In this study, we employed poly(A) tag sequencing (PAT-seq) to identify over 1500 transcripts whose expression exhibited significant alterations in response to HS, mediated by SIZ1, a SUMO E3 ligase in Arabidopsis. Further analysis revealed that more than 300 switch genes with varying poly(A) site usages were differentially expressed under HS conditions. Compared to non-canonical poly(A) sites, more genes utilize 3'UTR sites to regulate transcript expression by altering the usage of poly(A) signals. Based on the information of APA genes regulated by SIZ1, we selected two genes, Galactinol synthase enzyme (GolS2) and Tetratricopeptide repeat (TPR) like 3 (TTL3), for characterizing their novel functions. Overexpression of the distal transcript of GolS2 or the proximal transcript of TTL3 enhanced heat tolerance in Arabidopsis. Collectively, our current study elucidates the regulation of APA mediated by SIZ1 during HS response and establishes a strategy for identifying specific transcripts arising from APA for plant heat tolerance.