Alternative Polyadenylation Landscape Highlights its Critical Roles in Fine-tuning Cadmium Stress Response in Rice

Cadmium stress is one of the most critical factors affecting rice growth and development due to environmental pollution. Alternative polyadenylation (APA) plays essential roles in regulating plant gene expression and protein translation. Comprehensive understanding of APA response mechanisms under cadmium stress holds significant importance. We performed APA dynamics analysis in rice under cadmium stress using RNA-seq data from the SRA public database. The results revealed: 1) Cadmium stress induced widespread poly(A) site switching with differences between roots and shoots and temporal variations in APA patterns during prolonged stress exposure. Notably, the numbers of APA events raised significantly with the increasement of cadmium concentrations. What’s more, low and ultra-low cadmium concentrations preferentially promoted proximal poly(A) site selection across multiple genes, accompanied with significant transcriptional level changes. 2) APA regulated genes coupled with down-regulated expression were enriched in the photosynthetic components in rice shoots. Concurrently, significant transcriptional regulated genes with APA events were observed in reactive oxygen species scavenging, signal transduction pathways and protein synthesis machinery. 3) Expression profiles of polyadenylation factors were regulated under cadmium stress, suggesting their potential involvement in mediating APA alterations in downstream genes. 4) Among genes selecting distal poly(A) sites, we identified enriched miRNA target sites within extended 3'UTR regions, suggesting that miRNA binding to these extended regions may destabilize transcript isoforms, thereby contributing to their reduced expression levels. These findings provide valuable candidate genes and theoretical frameworks for elucidating APA-mediated regulatory networks in response to cadmium stress.