CHD7 Targets Active Gene Enhancer Elements to Modulate ES Cell- Specific Gene Expression
CHD7 Targets Active Gene Enhancer Elements to Modulate ES Cell- Specific Gene Expression
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DOI：
10.1371/journal.pgen.1001023
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发表时间：
2010-07-01
期刊：
影响因子：
4.5
通讯作者：
Scacheri, Peter C.
中科院分区：
文献类型：
--
作者：
Schnetz, Michael P.;Handoko, Lusy;Scacheri, Peter C.
CHD7是在哺乳动物细胞中发现的依赖于ATP的染色质重塑酶的染色域解旋酶DNA结合域家族的九个成员之一。CHD7的从头突变是Charge综合征的主要原因，Charge综合征是一种以多种先天性异常为特征的遗传疾病。为了深入了解CHD7的功能，我们使用染色质免疫沉淀和大规模平行DNA测序(CHIP-SEQ)技术在小鼠ES细胞中定位CHD7位点。我们确定了CHD7与染色质结合的10,483个位点。大多数CHD7位点显示出基因增强子元件的特征。具体地说，CHD7位点主要位于转录起始点的远端，包含高水平的H3K4单甲基化，发现于对DNase I消化高度敏感的开放染色质中，并与ES细胞特异性基因表达相关。此外，CHD7与P300共定位，P300是一种已知的增强子结合蛋白，也是增强子活性的有力预测因子。与CHIP-SEQ在小鼠ES细胞中定位的其他18个因子的相关性表明，CHD7还与ES细胞主调控因子OCT4、SOX2和NANOG共定位。CHD7位点与从CHD7(+/+)、CHD7(+/-)和CHD7(-/-)ES细胞获得的整体基因表达谱之间的相关性表明，CHD7在增强子中作为转录变阻器来调节或微调ES特异性基因的表达水平。CHD7可以正向或负向调节基因，尽管负调节似乎是CHD7结合的更直接的影响。这些数据表明，增强子结合蛋白可以限制基因的表达，并不一定是共激活因子。虽然ES细胞不太可能在Charge综合征中受到影响，但我们认为增强子介导的基因失调参与了疾病的发病机制，关键的CHD7靶基因可能受到正向或负向调控。
CHD7 is one of nine members of the chromodomain helicase DNA-binding domain family of ATP-dependent chromatin remodeling enzymes found in mammalian cells. De novo mutation of CHD7 is a major cause of CHARGE syndrome, a genetic condition characterized by multiple congenital anomalies. To gain insights to the function of CHD7, we used the technique of chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-Seq) to map CHD7 sites in mouse ES cells. We identified 10,483 sites on chromatin bound by CHD7 at high confidence. Most of the CHD7 sites show features of gene enhancer elements. Specifically, CHD7 sites are predominantly located distal to transcription start sites, contain high levels of H3K4 mono-methylation, found within open chromatin that is hypersensitive to DNase I digestion, and correlate with ES cell-specific gene expression. Moreover, CHD7 co-localizes with P300, a known enhancer-binding protein and strong predictor of enhancer activity. Correlations with 18 other factors mapped by ChIP-seq in mouse ES cells indicate that CHD7 also co-localizes with ES cell master regulators OCT4, SOX2, and NANOG. Correlations between CHD7 sites and global gene expression profiles obtained from Chd7(+/+), Chd7(+/-), and Chd7(-/-) ES cells indicate that CHD7 functions at enhancers as a transcriptional rheostat to modulate, or fine-tune the expression levels of ES-specific genes. CHD7 can modulate genes in either the positive or negative direction, although negative regulation appears to be the more direct effect of CHD7 binding. These data indicate that enhancer-binding proteins can limit gene expression and are not necessarily co-activators. Although ES cells are not likely to be affected in CHARGE syndrome, we propose that enhancer-mediated gene dysregulation contributes to disease pathogenesis and that the critical CHD7 target genes may be subject to positive or negative regulation.