Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)

摘要

Chromatin immunoprecipitation (ChIP) is a powerful technique to study interactions between transcription factors (TFs) and DNANA in vivo. For genome-wide de novo discovery of TF-binding sites, the DNANA that is obtained in ChIP experiments needs to be processed for sequence identification. The sequences can be identified by direct sequencing (ChIP-SESEQ) or hybridization to microarrays (ChIP-CHIP). Given the small amounts of DNANA that are usually obtained in ChIP experiments, successful and reproducible sample processing is challenging. Here we provide a detailed procedure for ChIP of plant TFs, as well as protocols for sample preparation for ChIP-SESEQ and for ChIP-CHIP. Our ChIP procedure is optimized for high signal-to-noise ratio starting with tissue fixation, followed by nuclei isolation, immunoprecipitation, DNANA amplification and purification. We also provide a guide for primary data analysis of ChIP-SESEQ data. The complete protocol for ChIP-SESEQ/ChIP-CHIP sample preparation starting from plant harvest takes ~7 d.