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 programs 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. Among these, we show that installing histone H3 lysine 4 trimethylation (H3K4me3) at promoters can causally instruct transcription 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 that co-targeted H3K27 trimethylation (H3K27me3) and H2AK119 monoubiquitination (H2AK119ub) maximizes 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.

染色质修饰与基因表达的调节模式有关，但它们的因果作用和对转录的上下文依赖性影响仍未解决。在这里，我们开发了一个模块化表观基因组编辑平台，该平台可以对九种关键染色质修饰或其组合进行编程，以精确定位活细胞中的位点。我们将其与单细胞读数结合起来，系统地定量每个特定染色质修饰引起的转录反应的幅度和异质性。其中，我们发现在启动子处安装组蛋白 H3 赖氨酸 4 三甲基化 (H3K4me3) 可以通过分层重塑染色质景观来因果地指导转录。我们进一步剖析 DNA 序列基序如何影响染色质标记的转录影响，识别不同顺式背景下的开关样和衰减效应。最后，我们检查了组合修饰的相互作用，揭示了共靶向 H3K27 三甲基化 (H3K27me3) 和 H2AK119 单泛素化 (H2AK119ub) 最大限度地提高了单细胞的沉默外显率。我们的精确扰动策略揭示了染色质修饰如何影响转录的因果原理，并剖析了如何通过上下文相互作用来校准定量响应。