Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
Methods Mol Biol. 2025;2873:93-109. doi: 10.1007/978-1-0716-4228-3_6.
Various proteins interact with specific genome regions, playing crucial roles in gene regulation. Chromatin Immunoprecipitation (ChIP) is the most commonly used method to study protein-DNA interactions in vivo. By combining ChIP with high-throughput sequencing, ChIP-seq allows for studying the genome-wide localization of proteins. Although several ChIP protocols are available for plant tissues, they are primarily designed for histone modifications and abundant proteins with high DNA-binding affinity, which are considered as the "standard targets." Here we describe a ChIP protocol for plant tissues not only optimized for the standard targets but also adapted for proteins with low abundances or weak DNA-binding ability. Successful execution of the protocol enables reliable generation of DNA templates for quantitative PCR or libraries for next-generation sequencing, which makes it an effective tool for analyzing genomic interactions of a wide range of proteins.
各种蛋白质与特定的基因组区域相互作用，在基因调控中发挥着关键作用。染色质免疫沉淀（ChIP）是研究体内蛋白质-DNA 相互作用最常用的方法。通过将 ChIP 与高通量测序相结合，ChIP-seq 可以研究蛋白质在全基因组范围内的定位。尽管有几种适用于植物组织的 ChIP 方案，但它们主要是针对组蛋白修饰和具有高 DNA 结合亲和力的丰富蛋白质设计的，这些蛋白质被认为是“标准靶标”。在这里，我们描述了一种不仅针对标准靶标进行了优化，而且还适用于丰度低或 DNA 结合能力弱的蛋白质的植物组织 ChIP 方案。该方案的成功执行可以为定量 PCR 生成可靠的 DNA 模板，或为下一代测序生成文库，使其成为分析广泛的蛋白质的基因组相互作用的有效工具。
