Quantitative analysis of chromatin accessibility in mouse embryonic fibroblasts
Quantitative analysis of chromatin accessibility in mouse embryonic fibroblasts
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小鼠胚胎成纤维细胞染色质可及性的定量分析
DOI：
10.1016/j.bbrc.2017.08.065
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发表时间：
2017
影响因子：
3.1
通讯作者：
Xu Xueqing
中科院分区：
文献类型：
--
作者：
Zhuo Baowen;Yu Juan;Chang Luyuan;Lei Jiafan;Wen Zengqi;Liu Cuifang;Mao Guankun;Wang Kehui;Shen Jie;Xu Xueqing
真核细胞的基因组DNA被组蛋白分级包装到染色质中。染色质纤维的动态组织在基因转录和其他DNA相关生物过程的调节中起着关键作用。最近，已经开发了许多方法来通过表征全基因组范围内的染色质附件来绘制染色质组织。然而，可靠的方法来定量映射染色质的可及性还没有得到很好的建立，特别是不是在全基因组规模。在这里，我们开发了一种用于小鼠胚胎成纤维细胞的修饰的MNase-seq，其中染色质使用微球菌核酸酶（MNase）在多个消化时间部分消化，允许定量分析局部但全基因组染色质压实。我们的研究结果提供了强有力的证据，在启动子区域的染色质可及性与基因活性呈正相关。总之，我们的检测是一个理想的工具，定量研究基因调控的角度染色质可及性。
Genomic DNA of eukaryotic cells is hierarchically packaged into chromatin by histones. The dynamic organization of chromatin fibers plays a critical role in the regulation of gene transcription and other DNA-associated biological processes. Recently, numerous approaches have been developed to map the chromatin organization by characterizing chromatin accessibilities in genome-wide. However, reliable methods to quantitatively map chromatin accessibility are not well-established, especially not on a genome-wide scale. Here, we developed a modified MNase-seq for mouse embryonic fibroblasts, wherein chromatin was partially digested at multiple digestion times using micrococcal nuclease (MNase), allowing quantitative analysis of local yet genome-wide chromatin compaction. Our results provide strong evidence that the chromatin accessibility at promoter regions are positively correlated with gene activity. In conclusion, our assay is an ideal tool for the quantitative study of gene regulation in the perspective of chromatin accessibility.