High-resolution mapping of h1 linker histone variants in embryonic stem cells.
High-resolution mapping of h1 linker histone variants in embryonic stem cells.
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DOI：
10.1371/journal.pgen.1003417
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发表时间：
2013
期刊：
影响因子：
4.5
通讯作者：
Fan Y
中科院分区：
文献类型：
--
作者：
Cao K;Lailler N;Zhang Y;Kumar A;Uppal K;Liu Z;Lee EK;Wu H;Medrzycki M;Pan C;Ho PY;Cooper GP Jr;Dong X;Bock C;Bouhassira EE;Fan Y
H1接头组蛋白促进染色质的高阶折叠，对哺乳动物的发育至关重要。为了实现H1变体H1 d和H1 c在胚胎干细胞（ESC）中的高分辨率映射，我们已经建立了一个敲入系统，并表明N-末端标记的H1蛋白在体内与其内源性对应物在功能上是可互换的。H1 d和H1 c从GC和基因丰富的区域和活性启动子中耗尽，与H3 K4 me 3负相关，但与H3 K9 me 3正相关，并与特征序列特征相关。令人惊讶的是，H1 d和H1 c在主要卫星上显着富集，与大量染色质相比，这些卫星显示出增加的核小体间距。虽然也耗尽在活跃的启动子和丰富的主要卫星，过表达的H10显示差异结合模式，在特定的重复序列相比，H1 d和H1 c。耗尽H1 c，H1 d，和H1 e的原因pericentric chromocenter聚类和去阻遏的主要卫星。这些结果整合了一个未充分研究的类型的染色质蛋白，即H1变体，到小鼠胚胎干细胞的表观基因组图谱的本地化，我们确定了显着的变化，在此表观遗传标记耗尽后，在臂间异染色质。胚胎干细胞（ESC）具有独特的染色质和表观遗传特征，这在定义多能干细胞的身份和基因组可塑性方面非常重要。虽然ESC表观基因组已被广泛的特点，组蛋白H1变体，染色质结构蛋白促进高阶染色质折叠的基因组定位，仍然难以捉摸。接头组蛋白H1是哺乳动物发育所必需的，并调节ESCs中特定基因的表达。在这里，通过使用与ChIP-seq相结合的敲入系统，我们首先在小鼠ESC中实现了两个H1变体在全基因组范围内的高分辨率定位。我们的研究揭示了这个未被探索的组蛋白家族与其他表观遗传标记和基因组属性的相关性。令人惊讶的是，我们确定了显着丰富的H1 d和H1 c的主要卫星序列。H10，映射使用过表达ESC线，显示出类似的功能，在活跃的启动子，但在重复序列的差异结合相比，H1 d和H1 c。此外，使用突变的胚胎干细胞是缺乏多个H1变体，我们证明了H1的作用，在染色中心聚类和转录抑制的主要卫星。因此，这些结果将这个重要的抑制性标记与已被充分理解的ESC表观基因组联系起来，并确定了H1在哺乳动物基因组组织中的新功能。
H1 linker histones facilitate higher-order chromatin folding and are essential for mammalian development. To achieve high-resolution mapping of H1 variants H1d and H1c in embryonic stem cells (ESCs), we have established a knock-in system and shown that the N-terminally tagged H1 proteins are functionally interchangeable to their endogenous counterparts in vivo. H1d and H1c are depleted from GC- and gene-rich regions and active promoters, inversely correlated with H3K4me3, but positively correlated with H3K9me3 and associated with characteristic sequence features. Surprisingly, both H1d and H1c are significantly enriched at major satellites, which display increased nucleosome spacing compared with bulk chromatin. While also depleted at active promoters and enriched at major satellites, overexpressed H10 displays differential binding patterns in specific repetitive sequences compared with H1d and H1c. Depletion of H1c, H1d, and H1e causes pericentric chromocenter clustering and de-repression of major satellites. These results integrate the localization of an understudied type of chromatin proteins, namely the H1 variants, into the epigenome map of mouse ESCs, and we identify significant changes at pericentric heterochromatin upon depletion of this epigenetic mark. Embryonic stem cells (ESCs) possess unique chromatin and epigenetic signatures, which are important in defining the identity and genome plasticity of pluripotent stem cells. Although ESC epigenomes have been extensively characterized, the genome localization of histone H1 variants, the chromatin structural proteins facilitating higher-order chromatin folding, remains elusive. Linker histone H1 is essential for mammalian development and regulates the expression of specific genes in ESCs. Here, by using a knock-in system coupled with ChIP–seq, we first achieve the high resolution mapping of two H1 variants on a genome-wide scale in mouse ESCs. Our study reveals the correlations of this underexplored histone family with other epigenetic marks and genome attributes. Surprisingly, we identify a dramatic enrichment of H1d and H1c at major satellite sequences. H10, mapped using an overexpressing ESC line, shows similar features at active promoters but differential binding at repetitive sequences compared with H1d and H1c. Furthermore, using mutant ESCs that are deficient for multiple H1 variants, we demonstrate the role of H1 in chromocenter clustering and transcriptional repression of major satellites. Thus, these results connect this important repressive mark with the well understood ESC epigenome and identify novel functions of H1 in mammalian genome organization.