Chromatin states and genomic organization impact replication timing and local patterns [ATAC-seq]. Chromatin states and genomic organization impact replication timing and local patterns [ATAC-seq]

Replication timing (RT) associates with genome architecture, while having a mixed relationship to histone marks. By profiling replication at high-resolution and systematically assessing broad and focused histone marks across cell cycle with and without genetic perturbation, we address the causal relationship between histone marks, their associated states and RT. Our approach identified four chromatin states, including a previously uncharacterized H3K36me2 state, that defined 97% of the mappable genome. RT and local replication patterns (e.g., initiation zones) quantitatively associate with chromatin states, histone mark dynamics, and spatial chromatin structure. Furthermore, overexpression of the histone H3 lysine 9/36 tri-demethylase KDM4A impacts RT genome-wide (11%), which is linked to KDM4A-associated histone marks and clusters of enhancer elements. Lastly, replication within H3K36me2-enriched neighborhoods is sensitive to KDM4A overexpression and is controlled at a megabase-scale. These studies establish a critical role for chromatin regulation in regulating RT and the local RT patterns. Overall design: Examination of replication timing in a replicate of RPE control or stably overexpressing KDM4A, at seven phases of cell cycle: ES, LS, G2/M, S1, S2, S3, S4

复制时序（Replication Timing, RT）与基因组架构密切相关，同时与组蛋白修饰存在复杂的关联关系。本研究通过高分辨率分析复制过程，并系统评估了存在/不存在遗传扰动时细胞周期各阶段的宽域与窄域组蛋白修饰，进而解析了组蛋白修饰、其关联染色质状态与复制时序之间的因果关系。本研究方法共鉴定出四种染色质状态，其中包含一种此前未被表征的H3K36me2状态，这些状态覆盖了97%的可比对基因组区域。复制时序与局部复制模式（如复制起始区域）均与染色质状态、组蛋白修饰动态变化及空间染色质结构存在定量关联。此外，组蛋白H3赖氨酸9/36三去甲基化酶KDM4A的过表达会在全基因组范围内影响11%区域的复制时序，该效应与KDM4A靶向的组蛋白修饰及增强子元件簇密切相关。最后，富集H3K36me2的染色质区域内的复制过程对KDM4A过表达敏感，且其调控尺度可达兆碱基级别。本研究证实了染色质调控在复制时序及局部复制时序模式调控中的关键作用。实验设计：在RPE对照细胞系或稳定过表达KDM4A的RPE细胞系的重复样本中，检测细胞周期七个阶段（ES、LS、G2/M、S1、S2、S3、S4）的复制时序。