Profiling Protein–DNA Interactions by Chromatin Immunoprecipitation in Arabidopsis

Hendry Susila, Zeeshan Nasim, Suhyun Jin, Geummin Youn, Hyewon Jeong, Ji Yul Jung, Ji Hoon Ahn

Research output: Chapter in Book/Report/Conference proceedingChapter

4 Citations (Scopus)


In plant cells, transcription factors play an important role in the regulation of gene expression, which eventually leads to the formation of complex phenotypes. Although chromatin immunoprecipitation (ChIP) involves a lengthy process that requires up to 4 days to complete, it is a powerful technique to investigate the interactions between transcription factors and their target sequences in vivo. Here, we describe a detailed ChIP protocol, focusing on ChIP-qPCR, from material collection to data analyses. Moreover, we explain multiple checkpoints for the quality control of ChIP-qPCR data to ensure the success of this protocol. As this protocol is robust, it can be adapted to other plant materials and plant species, and it can be used for genome-wide profiling experiments, including ChIP-chip and ChIP-seq analyses. We believe that our ChIP-qPCR protocol facilitates research on the interactions between plant transcription factors and their target sequences in vivo.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages12
Publication statusPublished - 2021

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Bibliographical note

Publisher Copyright:
© 2021, Springer Science+Business Media, LLC, part of Springer Nature.


  • Arabidopsis
  • Chromatin immunoprecipitation (ChIP)
  • Protein–DNA interactions

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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