ChIP-seq: A Powerful Tool for Studying Protein–DNA Interactions in Plants

DNA-binding proteins, including transcription factors, epigenetic and chromatin modifiers, control gene expression in plants. To map the binding sites of DNA-binding proteins in the genome is crucial for decoding gene regulatory networks. Chromatin immunoprecipitation (ChIP) followed by highthroughput DNA sequencing (ChIP-seq) is a widely used approach to identify the DNA regions bound by a specific protein in vivo. The information generated from ChIP-seq has tremendously advanced our understanding of the mechanisms of transcription factors, cofactors and histone modifications in regulating gene expression. In this review, we reviewed the recent research advances of ChIP-seq in plants, including a description of the ChIP-seq workflow and its various applications in plants, and in addition, provided a perspective for the potential advances of ChIP-seq.