Systematic Epigenome Editing Captures the Context-dependent Instructive Function of Chromatin Modifications

Abstract

Chromatin modifications are linked with regulating patterns of gene expression, but their causal role and context-dependent impact on transcription remains unresolved. Here, we develop a modular epigenome editing platform that programmes nine key chromatin modifications - or combinations thereof - to precise loci in living cells. We couple this with single-cell readouts to systematically quantitate the magnitude and heterogeneity of transcriptional responses elicited by each specific chromatin modification. Amongst these, we show installing H3K4me3 at promoters causally instructs transcription activation by hierarchically remodeling the chromatin landscape. We further dissect how DNA sequence motifs influence the transcriptional impact of chromatin marks, identifying switch-like and attenuative effects within distinct cis contexts. Finally, we examine the interplay of combinatorial modifications, revealing co-targeted H3K27me3 and H2AK119ub maximise silencing penetrance across single-cells. Our precision perturbation strategy unveils the causal principles of how chromatin modification(s) influence transcription, and dissects how quantitative responses are calibrated by contextual interactions.