Chromatin immunoprecipitation sequencing (ChIP-seq) for transcription factors and chromatin factors in Arabidopsis thaliana roots: From material collection to data analysis

Abstract

© 2018, Springer Science+Business Media, LLC. Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) is a powerful technique to investigate in vivo transcription factor (TF) binding to DNA, as well as chromatin marks. Here we provide a detailed protocol for all the key steps to perform ChIP-seq in Arabidopsis thaliana roots, also working on other A. thaliana tissues and in most non-ligneous plants. We detail all steps from material collection, fixation, chromatin preparation, immunoprecipitation, library preparation, and finally computational analysis based on a combination of publicly available tools.