|Title||Characterization of in vivo DNA-binding events of plant transcription factors by ChIP-seq : Experimental protocol and computational analysis|
|Author(s)||Mourik, Hilda Van; Muiño, J.M.; Pajoro, Alice; Angenent, G.C.; Kaufmann, Kerstin|
|Source||In: Plant Functional Genomics: Methods and Protocols: Second Edition Springer New York LLC - ISBN 9781493924448 - p. 93 - 121.|
Laboratory of Molecular Biology
PRI BIOS Plant Development Systems
|Publication type||Peer reviewed book chapter|
|Keyword(s)||ChIP-seq data analysis - Chromatin immunoprecipitation - Plant transcription factors - Transcription factor DNA-binding sites|
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 DNAfragments 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.