Characterization of in vivo DNA-binding events of plant transcription factors by ChIP-seq: experimental protocol and computational analysis.

Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a powerful technique for genome-wide identification of in vivo binding sites of DNA-binding proteins. The technique had been used to study many DNA-binding proteins in a broad variety of species. The basis of the ChIP-seq technique is the ability to covalently cross-link DNA and proteins that are located in very close proximity. This allows the use of an antibody against the (tagged) protein of interest to specifically enrich DNA-fragments bound by this protein. ChIP-seq can be performed using antibodies against the native protein or against tagged proteins. Using a specific antibody against a tag to immunoprecipitate tagged proteins eliminates the need for a specific antibody against the native protein and allows more experimental flexibility. In this chapter we present a complete workflow for experimental procedure and bioinformatic analysis that allows wet-lab biologists to perform and analyze ChIP-seq experiments.