Methods for ChIP-seq analysis: A practical workflow and advanced applications
Methods for ChIP-seq analysis: A practical workflow and advanced applications
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DOI：
10.1016/j.ymeth.2020.03.005
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发表时间：
2021-02-23
期刊：
影响因子：
4.8
通讯作者：
Sakata, Toyonori
中科院分区：
文献类型：
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作者：
Nakato, Ryuichiro;Sakata, Toyonori
染色质免疫沉淀测序（ChIP-seq）是表观基因组学研究的核心方法。组蛋白修饰的全基因组分析，例如增强子分析和全基因组染色质状态注释，使得能够系统地分析表观基因组景观如何有助于细胞身份、发育、谱系特化和疾病。在本文中，我们首先介绍了一个典型的ChIP-seq分析工作流程，从质量评估到染色质状态注释。我们专注于实践，而不是理论，生物学研究的方法。接下来，我们概述了各种先进的ChIP-seq应用，并介绍了几种最先进的方法，包括从表观基因组数据和数据填补预测基因表达水平和染色质环。最后，我们讨论了最近开发的单细胞ChIP-seq分析方法，阐明了复杂组织和癌症中的细胞多样性。
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a central method in epigenomic research. Genome-wide analysis of histone modifications, such as enhancer analysis and genome-wide chromatin state annotation, enables systematic analysis of how the epigenomic landscape contributes to cell identity, development, lineage specification, and disease. In this review, we first present a typical ChIP-seq analysis workflow, from quality assessment to chromatin-state annotation. We focus on practical, rather than theoretical, approaches for biological studies. Next, we outline various advanced ChIP-seq applications and introduce several state-of-the-art methods, including prediction of gene expression level and chromatin loops from epigenome data and data imputation. Finally, we discuss recently developed single-cell ChIP-seq analysis methodologies that elucidate the cellular diversity within complex tissues and cancers.