Chromatin Immunoprecipitation Sequencing (ChIP-Seq) for Transcription Factors and Chromatin Factors in Arabidopsis thaliana Roots: From Material Collection to Data Analysis

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1761)

Abstract

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.

Key words

Chromatin immunoprecipitation (ChIP) Chromatin Transcription factor (TF) Next-generation sequencing Arabidopsis Root Bioinformatics 

Notes

Acknowledgment

S.C. was supported by an EMBO long-term fellowship (ALTF 290-2013). V.C. lab is supported by the Thailand Research Fund (TRF) Grant for New Scholar (MRG6080235); Newton Advanced Fellowship through TRF (DBG60800003) and Royal Society (NA160153); the Faculty of Science, Mahidol University; and the Crown Property Bureau Foundation. The Wigge lab is supported by the Gatsby Charitable Foundation, the European Research Council, and the Biotechnology and Biological Sciences Research Council. The authors have no conflict of interest.

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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  1. 1.The Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
  2. 2.Department of Biochemistry, Faculty of ScienceMahidol UniversityBangkokThailand
  3. 3.Integrative Computational BioScience (ICBS) CenterMahidol UniversityNakhon PathomThailand
  4. 4.Systems Biology of Diseases Research Unit, Faculty of ScienceMahidol UniversityNakhon PathomThailand
  5. 5.Laboratoire de Reproduction et Développement des Plantes – ENS LyonLyon Cedex 07France

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