Abstract
Alternative polyadenylation (APA) is a widespread post-transcriptional regulation that generates transcripts with variable 3' untranslated region (UTR) lengths. In this study, poly(A)-tag sequencing (PAT-seq) was performed during the process of Magnaporthe oryzae infection of rice. Genome-wide dynamic changes of APA profiles were identified during the response, with widespread shortening of gene transcripts. Shortened genes were found to function in biological processes associated with stress responses. Importantly, the changes of 3' UTR length were negatively related to the expression levels of the corresponding genes. In addition, we found that the expression levels of miRNAs that bind to the 3' UTRs of the APA genes were negatively correlated with the expression levels of the corresponding APA genes. This correlation suggests a potential regulatory strategy where immune-related genes might evade miRNA-mediated repression via 3' UTR shortening. To assess the biological impact of these APA dynamics, we functionally characterised a representative candidate, Os05g0509500, that exhibits complex and dynamic APA site switching upon infection. Knockout of Os05g0509500 via CRISPR/Cas9 revealed its positive regulatory role in rice blast, offering initial insights into the function of APA in this disease. Several core polyadenylation protein factors were significantly differentially expressed during the rice response. Our results revealed that the precise transcriptome-wide poly(A) site selection of genes during rice blast challenge, and the relationships between miRNAs and targeted APA genes, are tightly regulated. Such a mechanism provides a new perspective for designing novel strategies to control rice blast disease.