Lineage-specific retrotransposon co-option reveals a conserved ASH2L isoform as an epigenetic primer of developmental gene promoters

Abstract How pluripotent stem cells pre-configure the chromatin landscape to enable timely activation of developmental gene programs remains a central question in developmental biology. Here we demonstrate that the core chromatin regulator ASH2L undergoes a developmentally regulated transcription start site (TSS) switch that generates two protein isoforms with distinct developmental functions: a full-length ASH2L containing an N-terminal intrinsically disordered region (IDR), and a conserved, truncated protein isoform lacking this region. In mouse pluripotent stem cells, a lineage-specific ERV-K retrotransposon drives the upstream TSS, which suppresses the downstream TSS through transcription-coupled SETD2-mediated histone H3 lysine 36 methylation. The resulting stem cell–specific truncated ASH2L assembles into COMPASS complexes and enhances histone H3 lysine 4 trimethylation at promoters governing early development. Despite being restricted to pluripotent stem cells, truncated ASH2L is required for proper axial patterning in gastruloids and for the transition of neural progenitors to motor neurons. This temporal decoupling, wherein a chromatin state established during pluripotency executes its function only after the establishing isoform disappears, defines an epigenetic priming mechanism for developmental timing. Thus, lineage-specific retrotransposon co-option reveals how a dedicated protein isoform configures the pluripotent epigenome for developmental transitions after its own expression has ceased.