Studying Transcription Factor Binding to Specific Genomic Loci by Chromatin Immunoprecipitation (ChIP)

Plant hormone signaling involves complex transcriptional networks, where transcription factors orchestrate the control of specific gene expression. These networks include cross talk between hormone signaling pathways, and the integration of environmental signals and the developmental program. Understanding how particular transcription factors respond and integrate specific signals is crucial in order to understand the basic mechanisms of hormonal signaling and cross talk. Studying transcription factor binding at specific genomic loci by chromatin immunoprecipitation (ChIP) is therefore a valuable technique in order to analyze transcriptional regulation. The method is based on cross-linking proteins to DNA, the isolation of chromatin, and immunoprecipitation of a transcription factor of interest. The attached DNA is then recovered and analyzed by quantitative real-time PCR in order to establish binding sites of the respective transcription factor. Here, we present a relatively simple and short protocol for ChIP on single loci.