Characterization of In Vivo DNA-Binding Events of Plant Transcription Factors by ChIP-seq: Experimental Protocol and Computational Analysis

  • Hilda van Mourik
  • Jose M. Muiño
  • Alice Pajoro
  • Gerco C. Angenent
  • Kerstin KaufmannEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1284)


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.

Key words

Chromatin immunoprecipitation ChIP-seq data analysis Plant transcription factors Transcription factor DNA-binding sites 


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Hilda van Mourik
    • 1
  • Jose M. Muiño
    • 2
  • Alice Pajoro
    • 1
  • Gerco C. Angenent
    • 1
    • 3
  • Kerstin Kaufmann
    • 1
    • 4
    Email author
  1. 1.Laboratory of Molecular BiologyWageningen UniversityWageningenThe Netherlands
  2. 2.Department of Computational Molecular BiologyMax Planck Institute for Molecular GeneticsBerlinGermany
  3. 3.Business Unit BiosciencePlant Research InternationalWageningenThe Netherlands
  4. 4.Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany

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