Ostrow A Zachary, Viggiani Christopher J, Aparicio Jennifer G, Aparicio Oscar M
Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.
Methods Mol Biol. 2015;1300:155-68. doi: 10.1007/978-1-4939-2596-4_11.
Chromatin immunoprecipitation (ChIP) is a widely used method to study interactions between proteins and discrete chromosomal loci in vivo. ChIP was originally developed for in vivo analysis of protein associations with candidate DNA sequences known or suspected to bind the protein of interest. The advent of DNA microarrays enabled the unbiased, genome-scale identification of all DNA sequences enriched by ChIP, providing a genomic map of a protein's chromatin binding. This method, termed ChIP-chip, is broadly applicable and has been particularly valuable in DNA replication studies to map potential replication origins in Saccharomyces cerevisiae and other organisms based on the specific association of certain replication proteins with these chromosomal elements, which are distributed throughout the genome. More recently, high-throughput sequencing (HTS) technologies have replaced microarrays as the preferred method for genomic analysis of ChIP experiments, and this combination is termed ChIP-Seq. We present a detailed ChIP-Seq protocol for S. cerevisiae that can be adapted for different HTS platforms and for different organisms. We also outline general schemes for data analysis; however, HTS data analyses usually must be tailored specifically for individual studies, depending on the experimental design, data characteristics, and the genome being analyzed.
染色质免疫沉淀（ChIP）是一种广泛应用于研究体内蛋白质与离散染色体位点之间相互作用的方法。ChIP最初是为体内分析蛋白质与已知或疑似结合目标蛋白的候选DNA序列的关联而开发的。DNA微阵列的出现使得能够无偏见地在全基因组范围内鉴定所有通过ChIP富集的DNA序列，从而提供了蛋白质染色质结合的基因组图谱。这种方法被称为ChIP芯片，具有广泛的适用性，在DNA复制研究中尤其有价值，可基于某些复制蛋白与分布于整个基因组的这些染色体元件的特异性关联，来绘制酿酒酵母和其他生物体中潜在的复制起点。最近，高通量测序（HTS）技术已取代微阵列成为ChIP实验基因组分析的首选方法，这种组合被称为ChIP-Seq。我们展示了一种适用于酿酒酵母的详细ChIP-Seq方案，该方案可适用于不同的HTS平台和不同的生物体。我们还概述了数据分析的一般方案；然而，HTS数据分析通常必须根据实验设计、数据特征和所分析的基因组，专门针对个别研究进行调整。
