ChIP-Seq to Analyze the Binding of Replication Proteins to Chromatin.
ChIP-Seq to Analyze the Binding of Replication Proteins to Chromatin.
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DOI：
10.1007/978-1-4939-2596-4_11
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发表时间：
2015-01-01
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影响因子：
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通讯作者：
Aparicio, Oscar M
中科院分区：
文献类型：
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作者：
Ostrow, A Zachary;Viggiani, Christopher J;Aparicio, Oscar M
染色质免疫沉淀（ChIP）是一种广泛应用于体内研究蛋白质与离散染色体位点之间相互作用的方法。ChIP最初是为了在体内分析已知或怀疑与目标蛋白结合的候选DNA序列的蛋白质关联而开发的。DNA微阵列的出现使得通过ChIP富集的所有DNA序列的无偏倚、基因组规模的鉴定成为可能，从而提供了蛋白质染色质结合的基因组图谱。这种被称为ChIP-chip的方法广泛适用，在DNA复制研究中特别有价值，可以根据某些复制蛋白与这些分布在整个基因组中的染色体元件的特定关联来绘制酿酒酵母和其他生物体的潜在复制起源。最近，高通量测序（HTS）技术已经取代微阵列作为ChIP实验基因组分析的首选方法，这种组合被称为ChIP- seq。我们提出了一种详细的针对酿酒葡萄球菌的ChIP-Seq方案，该方案可以适用于不同的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、数据特征和被分析的基因组，专门为个别研究量身定制。
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.