Transcriptional interference drives intronic polyadenylation at the endogenous H13/Mcts2 locus

Over a tenth of mammalian genes are nested within other host genes, raising the question of how both can be co-expressed when concurrent transcription occurs in overlapping genetic space. DNA methylation at nested intragenic CpG island promoters can prevent such conflict by silencing the nested gene. Conversely, when these promoters lack DNA methylation and are active, transcriptional interference is widely assumed to occur, but this has not been mechanistically demonstrated at endogenous mammalian loci. Here, we demonstrate transcriptional interference at an endogenous mammalian host/nested locus, the imprinted H13/Mcts2 pair. Active nested gene (Mcts2) transcription promotes host gene (H13) intronic polyadenylation, but when the intragenic Mcts2 promoter is silenced through DNA methylation, host gene elongation reaches the distal 3'UTR polyadenylation of H13. We establish that this intronic polyadenylation depends on the act of transcription itself, independently of DNA methylation at the intragenic Mcts2 promoter. Moreover, nested gene transcription disrupts host gene elongation even when the upstream intronic polyadenylation signal is genetically ablated. Our findings provide mechanistic insight into the widely held assumption of transcriptional interference and reveal how nested gene transcription can trigger premature termination of host genes, with implications for the hundreds of similarly organised loci across mammalian genomes.