Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome
Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome
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DOI：
10.1016/j.celrep.2014.10.018
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发表时间：
2014-11-06
期刊：
影响因子：
8.8
通讯作者：
Guenther, Matthew G.
中科院分区：
文献类型：
--
作者：
Orlando, David A.;Chen, Mei Wei;Guenther, Matthew G.
染色质免疫沉淀结合大规模平行DNA测序（ChIP-seq）的表观基因组图谱分析是一种用于研究生物系统（如人类疾病）中基于染色质的调控的流行方法，但缺乏一种经验方法来实现实验之间的规范化，限制了该技术的准确性和实用性。在这里，我们描述了一种称为ChIP与参考外源基因组（ChIP- rx）的方法，该方法允许人们使用定义数量的参考表观基因组对细胞群体中的组蛋白修饰状态进行全基因组范围的定量比较。ChIP-Rx能够发现和量化哺乳动物细胞的动态表观基因组谱，否则使用传统的归一化方法仍然是隐藏的。我们展示了这种方法在测量化学扰动后表观基因组变化的实用性，并展示了ChIP-seq实验的参考归一化如何能够发现组蛋白修饰占用的疾病相关变化。
Epigenomic profiling by chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq) is a prevailing methodology used to investigate chromatin-based regulation in biological systems such as human disease, but the lack of an empirical methodology to enable normalization among experiments has limited the precision and usefulness of this technique. Here, we describe a method called ChIP with reference exogenous genome (ChIP-Rx) that allows one to perform genome-wide quantitative comparisons of histone modification status across cell populations using defined quantities of a reference epigenome. ChIP-Rx enables the discovery and quantification of dynamic epigenomic profiles across mammalian cells that would otherwise remain hidden using traditional normalization methods. We demonstrate the utility of this method for measuring epigenomic changes following chemical perturbations and show how reference normalization of ChIP-seq experiments enables the discovery of disease-relevant changes in histone modification occupancy.