A twin UGUA motif directs the balance between gene isoforms through CFIm and the mTORC1 signaling pathway.

Alternative polyadenylation (APA) generates mRNA isoforms and diversifies gene expression. Here we report the identification of a twin UGUA motif, UGUAYUGUA, and its function in APA. Applying cTag-PAPERCLIP to Tsc1 conditional knockout mice, we discovered that the mTORC1 pathway balances expression of Trim9 isoforms. We showed that CFIm components, CPSF6 and NUDT21, promote Trim9/TRIM9-S expression in mouse and human, and we identified an evolutionarily conserved UGUAYUGUA motif that is critical for this regulation. We found additional CPSF6-regulated polyadenylation sites (PASs) with similar twin UGUA motifs in human, and we experimentally validated the twin UGUA motif functionality in BMPR1B, MOB4, and BRD4-L. Importantly, we showed that inserting a twin UGUA motif into a heterologous PAS was sufficient to confer regulation by CPSF6 and mTORC1. Our study reveals an evolutionarily conserved mechanism to regulate gene isoform expression and implicates possible gene isoform imbalance in cancer and neurologic disorders with mTORC1 pathway dysregulation.