Sunset enhancers: tracing H3K27 acetylation on closed chromatin in myeloid lineage differentiation
Abstract
Understanding the relationship between histone modification and chromatin accessibility of enhancers is key to elucidating their impact on cell-type-specific gene expression during differentiation. Previous analyses found that enhancers in hematopoietic progenitor cells have a lower correlation between accessible chromatin and H3K4 monomethylation (H3K4me1) than terminal cell types. We used ATAC-seq, ChIP-seq, and RNA-seq data to track chromatin accessibility, H3K4 monomethylation (H3K4me1), and H3K27 acetylation (H3K27ac) status of 37,473 enhancers during myeloid differentiation, and assessed gene expression related to changes in enhancer status. We identified a subset of enhancers in multipotent progenitor cells that were both closed and marked by H3K27ac, a mark of active enhancers. A majority of this closed/H3K27ac enhancer subset (>80%) remains closed and subsequently loses its acetylation during differentiation into terminal cell types within the myeloid lineage. Based on the stepwise pattern of deactivation we have termed these features sunset enhancers. We found that each cell type has a nearly exclusive set of these sunset enhancers, and a significant proportion of closed/H3K27ac+ enhancers are not marked by H3K4me1. Genes proximal to sunset enhancers demonstrate an intermediate level of RNA expression (between genes proximal to closed/inactive and open/active enhancers). GO enrichment analysis reveals closed/H3K27ac+ (sunset) enhancers are associated with diverse biological processes across cell types. Analysis of genes associated with sunset enhancers in MPP cells that remain closed in downstream cell types indicates they likely do not contribute to myeloid lineage commitment in hematopoiesis. In conclusion, we have identified a new enhancer subset (closed/H3K27ac+) that is largely decommissioned in a stepwise manner during differentiation.
