Jordán-Pla Antonio, Visa Neus
Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20c, 10691, Stockholm, Sweden.
Methods Mol Biol. 2018;1689:9-28. doi: 10.1007/978-1-4939-7380-4_2.
Arguably one of the most valuable techniques to study chromatin organization, ChIP is the method of choice to map the contacts established between proteins and genomic DNA. Ever since its inception, more than 30 years ago, ChIP has been constantly evolving, improving, and expanding its capabilities and reach. Despite its widespread use by many laboratories across a wide variety of disciplines, ChIP assays can be sometimes challenging to design, and are often sensitive to variations in practical implementation.In this chapter, we provide a general overview of the ChIP method and its most common variations, with a special focus on ChIP-seq. We try to address some of the most important aspects that need to be taken into account in order to design and perform experiments that generate the most reproducible, high-quality data. Some of the main topics covered include the use of properly characterized antibodies, alternatives to chromatin preparation, the need for proper controls, and some recommendations about ChIP-seq data analysis.
染色质免疫沉淀（ChIP）可以说是研究染色质组织最有价值的技术之一，是绘制蛋白质与基因组DNA之间建立的相互作用图谱的首选方法。自30多年前问世以来，ChIP一直在不断发展、改进，并扩展其功能和应用范围。尽管许多实验室在广泛的学科领域中广泛使用ChIP分析，但有时设计ChIP分析具有挑战性，并且通常对实际操作中的变化很敏感。在本章中，我们将对ChIP方法及其最常见的变体进行概述，特别关注ChIP-seq。我们试图解决设计和进行实验时需要考虑的一些最重要的方面，以便生成最可重复、高质量的数据。涵盖的一些主要主题包括使用经过适当表征的抗体、染色质制备的替代方法、适当对照的必要性以及关于ChIP-seq数据分析的一些建议。
