Histone variant H2A.Z regulates nucleosome unwrapping and CTCF binding in mouse ES cells
Histone variant H2A.Z regulates nucleosome unwrapping and CTCF binding in mouse ES cells
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组蛋白变体 H2A.Z 调节小鼠 ES 细胞中的核小体解包和 CTCF 结合
DOI：
10.1093/nar/gkaa360
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发表时间：
2020-05
影响因子：
14.9
通讯作者：
Guohong Li
中科院分区：
文献类型：
--
作者：
Zengqi Wen;Liwei Zhang;Haihe Ruan;Guohong Li
摘要核小体是染色质的基本结构单位，其动力学在基因组功能调控中起着重要作用。然而，核小体的结构是如何调节组蛋白变体在体内仍然是在很大程度上未确定的。在这里，通过采用微球菌核酸酶（MNase）消化交联染色质，然后进行染色质免疫沉淀（ChIP）和配对末端测序（MNase-X-ChIP-seq），我们绘制了小鼠胚胎干（ES）细胞中含有组蛋白变体H2A.Z的核小体的解包状态。我们发现，H2 A. Z核小体更丰富的解包裹态相比，典型的核小体。有趣的是，与具有120-140 bp DNA的+1 H2 A. Z核小体相比，具有30-80 bp DNA的+1 H2 A. Z核小体与活性较低的基因相关。我们通过在小鼠ES细胞中CTCF CUT&RUN后H2A.Z和H2 A的re-ChIP证实了H2A.Z核小体在天然条件下的解包裹。重要的是，我们发现H2A.Z的消耗导致H3.3核小体的解包裹减少和CTCF结合增加。总之，通过MNase-X-ChIP-seq，我们表明组蛋白变体H2A.Z在体内调节核小体解包，并且其在调节转录或CTCF结合中的功能与H2A.Z核小体的解包状态相关。
Abstract Nucleosome is the basic structural unit of chromatin, and its dynamics plays critical roles in the regulation of genome functions. However, how the nucleosome structure is regulated by histone variants in vivo is still largely uncharacterized. Here, by employing Micrococcal nuclease (MNase) digestion of crosslinked chromatin followed by chromatin immunoprecipitation (ChIP) and paired-end sequencing (MNase-X-ChIP-seq), we mapped unwrapping states of nucleosomes containing histone variant H2A.Z in mouse embryonic stem (ES) cells. We found that H2A.Z nucleosomes are more enriched with unwrapping states compared with canonical nucleosomes. Interestingly, +1 H2A.Z nucleosomes with 30–80 bp DNA is correlated with less active genes compared with +1 H2A.Z nucleosomes with 120–140 bp DNA. We confirmed the unwrapping of H2A.Z nucleosomes under native condition by re-ChIP of H2A.Z and H2A after CTCF CUT&RUN in mouse ES cells. Importantly, we found that depletion of H2A.Z results in decreased unwrapping of H3.3 nucleosomes and increased CTCF binding. Taken together, through MNase-X-ChIP-seq, we showed that histone variant H2A.Z regulates nucleosome unwrapping in vivo and that its function in regulating transcription or CTCF binding is correlated with unwrapping states of H2A.Z nucleosomes.
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