Positioning of nucleosomes along DNA is an integral regulator of chromatin accessibility and gene expression in diverse cell types. However, the precise nature of how histone demethylases including the histone 3 lysine 4 (H3K4) demethylase, KDM5B, impacts nucleosome positioning around transcriptional start sites (TSS) of active genes is poorly understood. Here, we report that KDM5B is a critical regulator of nucleosome positioning in embryonic stem (ES) cells. Micrococcal nuclease sequencing (MNase-Seq) revealed increased enrichment of nucleosomes around TSS regions and DNase I hypersensitive sites in KDM5B-depleted ES cells. Moreover, depletion of KDM5B resulted in a widespread redistribution and disorganization of nucleosomes in a sequence-dependent manner. Dysregulated nucleosome phasing was also evident in KDM5B-depleted ES cells, including asynchronous nucleosome spacing surrounding TSS regions, where nucleosome variance was positively correlated with the degree of asynchronous phasing. The redistribution of nucleosomes around TSS regions in KDM5B-depleted ES cells is correlated with dysregulated gene expression, and altered H3K4me3 and RNA polymerase II occupancy. In addition, we found that DNA shape features varied significantly at regions with shifted nucleosomes. Altogether, our data support a role for KDM5B in regulating nucleosome positioning in ES cells.

中文翻译：

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H3K4脱甲基酶KDM5B对微球菌核酸酶测序揭示胚胎干细胞核小体组织的贡献

核小体沿DNA的定位是多种细胞类型中染色质可及性和基因表达的不可或缺的调节器。然而，人们对包括组蛋白3赖氨酸4（H3K4）脱甲基酶KDM5B在内的组蛋白脱甲基酶如何影响活性基因转录起始位点（TSS）周围的核小体定位的确切性质了解甚少。在这里，我们报告KDM5B是胚胎干（ES）细胞中核小体定位的关键调节剂。微球菌核酸酶测序（MNase-Seq）显示，在耗尽KDM5B的ES细胞中，TSS区和DNase I超敏位点周围的核小体富集度增加。此外，KDM5B的耗竭导致核小体以依赖序列的方式广泛分布和重组。在耗尽KDM5B的ES细胞中，核小体的定相失调也很明显，包括围绕TSS区域的异步核小体间距，其中核小体方差与异步定相程度呈正相关。耗尽KDM5B的ES细胞中TSS区域周围核小体的重新分布与基因表达失调，H3K4me3和RNA聚合酶II占有率发生改变有关。此外，我们发现DNA形状特征在核小体移位区域显着变化。总之，我们的数据支持KDM5B在调节ES细胞中核小体定位中的作用。并改变了H3K4me3和RNA聚合酶II的占有率。此外，我们发现DNA形状特征在核小体移位区域显着变化。总之，我们的数据支持KDM5B在调节ES细胞中核小体定位中的作用。并改变了H3K4me3和RNA聚合酶II的占有率。此外，我们发现DNA形状特征在核小体移位区域显着变化。总之，我们的数据支持KDM5B在调节ES细胞中核小体定位中的作用。