Single-cell chromatin landscapes visualize epigenetic barriers and reveal lineage-specific Polycomb-mediated repression

Abstract

Understanding how chromatin state contributes to developmental trajectories remains central to deciphering cell specification and differentiation. Using dual-modality nano-CUT&Tag, we profiled two antagonistic histone modifications--active H3K27ac and repressive H3K27me3--in thousands of single cells from Drosophila embryos across early lineage diversification and terminal differentiation. Joint embedding of both marks enabled robust cell-type classification and revealed increasing epigenetic specificity over developmental time. We ordered cells by developmental age and epigenomic similarity, and defined an epigenetic potential metric that visualizes repressive chromatin barriers as landscapes that predict transcriptional activity. While many genes conform to a classical model in which expression resides in low-potential epigenetic valleys, a substantial subset shows co-occurrence of H3K27ac, H3K27me3, and transcription within the same cell lineage. This indicates that Polycomb-mediated H3K27me3 repression frequently acts within, rather than solely between, lineages. Consistently, tissue-specific E(z) knockdown demonstrates that partial loss of H3K27me3 predominantly de-represses lineage-matched genes rather than inducing fate conversion. Systematic analysis showed that H3K27me3 occurs in multiple distributional modes, ranging from ubiquitous to highly cell-type-specific deposition, co-occuring with accessible but silent gene promoters. These findings demonstrate that cell-type-specific deployment of H3K27ac and H3K27me3 sculpts epigenetic potential landscapes that shape developmental gene expression patterns.