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

ABSTRACT: Over a tenth of mammalian genes are organised as nested within distinct host genes, questioning how both can be expressed when concurrent transcription can collide in the same genetic space. DNA methylation-mediated silencing of nested genes can prevent such conflict. Alternatively, transcriptional interference can occur, but this has not been mechanistically demonstrated independently of DNA methylation outside of artificial systems. We demonstrate transcriptional interference at an endogenous mammalian host/nested locus, the imprinted H13/Mcts2 pair. Here, active nested gene (Mcts2) transcription promotes host gene (H13) intronic polyadenylation, while Mcts2 silencing through promoter DNA methylation, favours distal 3′UTR polyadenylation. Using dCas9:KRAB-mediated silencing we establish that this effect depends on transcription itself, independently of DNA methylation. Moreover, nested gene transcription interferes with host gene elongation even when the upstream intronic polyadenylation site is ablated. Nested gene transcriptional interference can thus stimulate intronic termination of their host gene with implications for hundreds of loci. Allelic CUT&RUN was utilised to assay H3K36me3 to track elongation and H3K4me3 to assay promoters at the H13/Mcts2 locus within this study