Retrotransposon-driven co-transcriptional chromatin remodelling rewires Ash2l isoform usage to prime developmental promoters [ChIP-seq]

Transcription start site (TSS) selection diversifies the transcriptome and proteome, yet the mechanisms and functional consequences of alternative TSSs in development remain poorly understood. Here, we show that the chromatin regulator ASH2L undergoes developmentally regulated alternative TSS switching in differentiating mouse cells, generating distinct mRNA and protein isoforms: a full-length ASH2L and a truncated form lacking an intrinsically disordered region (IDR). In pluripotent stem cells, transcription from the upstream TSS is driven by a mouse-specific retrotransposon element that suppresses transcription from the downstream TSS through a transcription interference mechanism involving SETD2-directed histone H3 lysine 36 methylation. The resulting upstream-driven, stem cell–specific truncated ASH2L isoform primes developmental-gene promoters for histone H3 lysine 4 methylation, establishing a chromatin state required for embryogenesis and motor neuron differentiation. We propose that co-option of a mouse-specific retrotransposon drives a switch in Ash2l TSS and protein isoforms to control developmental timing and cell fate decisions.