MRE11 proximal polyadenylation site-mediated looping impacts transcription and genomic stability

Alternative polyadenylation (APA) generates transcript isoforms with variable 3' UTR lengths, but its regulatory role in DNA damage response (DDR) genes remains poorly understood. Here, we demonstrate that the proximal polyadenylation site (pPAS) of MRE11 engages in PAS-promoter looping to facilitate RNA polymerase recycling and maintain high promoter activity, a mechanism not well characterized in mammals. Deletion of the MRE11 pPAS disrupts this looping, reduces MRE11 transcription, impairs MRN complex levels, and phenocopies hypomorphic MRE11 mutations. MRE11pPAS-/- cells exhibit ectopic DNA replication and reduced viability under overgrowth conditions. EdU-seq revealed that aberrant DNA synthesis in MRE11pPAS-/- cells occurs primarily at intronic and intergenic regions. MRE11 ChIP-seq showed decreased binding at these regions, correlating with elevated DNA replication. Furthermore, several DDR genes with multiple PASs form PAS-promoter loops, suggesting a broader regulatory mechanism. Together, our findings establish the MRE11 pPAS as a critical noncoding element that maintains genome stability through transcriptional regulation via PAS-promoter looping.