H3K9me3 as a gatekeeper of lineage-specific enhancers in embryonic progenitor cells

While many studies of developmental control have focused on gene activation, less is known about the extent to which regulatory programs are actively repressed in progenitor cells. We previously showed that trimethylation of histone H3 at lysine 9 (H3K9me3) is a repressive mark that is remodeled on protein-coding genes when endodermal progenitors transition to liver and pancreatic β cell fates. Yet whether H3K9me3 is dynamic at promoters and enhancers has not been determined. Here we find that promoters of liver-specific genes are strongly enriched for H3K9me3 in undifferentiated progenitors, whereas such enrichment is not observed at promoters of more broadly expressed liver genes. We further show that enhancers specific to differentiated tissues-including liver, islet, and cerebral cortex-are strongly enriched for H3K9me3 in their corresponding tissue stem and progenitor cells. In hepatoblasts, H3K9me3 contributes to maintaining the undifferentiated state by restricting FOXA2 and HNF4α from binding to most enhancers, while there remain thousands of H3K9me3-marked enhancers where the factors are not restricted from binding. Our findings illustrate how H3K9me3-mediated heterochromatinization can restrict transcription factor engagement in progenitor cells to prevent inappropriate activation during early development. H3K9me3 at enhancers that allow transcription factor binding may reflect developmental competence.