Policarpi Cristina, Munafò Marzia, Tsagkris Stylianos, Carlini Valentina, Hackett Jamie A
Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy.
Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany.
Nat Genet. 2024 Jun;56(6):1168-1180. doi: 10.1038/s41588-024-01706-w. Epub 2024 May 9.
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调控模式相关联，但其因果作用以及对转录的上下文依赖性影响仍未得到解决。在此，我们开发了一个模块化表观基因组编辑平台，可将九种关键染色质修饰或其组合编程至活细胞中的精确位点。我们将此与单细胞读数相结合，以系统地定量每种特定染色质修饰引发的转录反应的幅度和异质性。在这些研究中，我们表明在启动子处安装组蛋白H3赖氨酸4三甲基化（H3K4me3）可通过分层重塑染色质景观来因果性地指导转录。我们进一步剖析了DNA序列基序如何影响染色质标记的转录影响，确定了不同顺式背景下的开关样和衰减效应。最后，我们研究了组合修饰的相互作用，发现共靶向的组蛋白H3赖氨酸27三甲基化（H3K27me3）和组蛋白H2A赖氨酸119单泛素化（H2AK119ub）可使单细胞中的沉默渗透率最大化。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，并剖析了定量反应如何通过上下文相互作用进行校准。
