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.

中文翻译：

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ChIP-seq 分析方法：实用的工作流程和高级应用

染色质免疫沉淀后测序 (ChIP-seq) 是表观基因组研究的核心方法。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，可以系统地分析表观基因组景观如何影响细胞身份、发育、谱系规范和疾病。在这篇综述中，我们首先展示了一个典型的 ChIP-seq 分析工作流程，从质量评估到染色质状态注释。我们专注于生物学研究的实用方法，而不是理论方法。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，包括根据表观基因组数据和数据插补预测基因表达水平和染色质环。最后，