Chromatin Immunoprecipitation for Detecting Epigenetic Marks on Plant Nucleosomes

  • Kiyotaka NagakiEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1469)


Due to high resolution and reproducibility, chromatin immunoprecipitation (ChIP) has been used as a standard tool to investigate epigenetic marks including modified histones and specific histone variants (e.g., centromere-specific histone H3, CENH3) in this decade. Here, I describe a sensitive and low-background ChIP protocol for a wide range of plant species.

Key words

Chromatin immunoprecipitation (ChIP) Epigenetic marks Histone modification Histone variants CENH3 


  1. 1.
    Nagaki K, Talbert PB, Zhong CX, Dawe RK, Henikoff S, Jiang JM (2003) Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. Genetics 163:1221–1225PubMedPubMedCentralGoogle Scholar
  2. 2.
    Zhong CX, Marshall JB, Topp C, Mroczek R, Kato A, Nagaki K, Birchler JA, Jiang J, Dawe RK (2002) Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell 14:2825–2836CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Houben A, Schroeder-Reiter E, Nagaki K, Nasuda S, Wanner G, Murata M, Endo TR (2007) CENH3 interacts with the centromeric retrotransposon cerebra and GC-rich satellites and locates to centromeric substructures in barley. Chromosoma 116:275–283CrossRefPubMedGoogle Scholar
  4. 4.
    Nagaki K, Murata M (2005) Characterization of CENH3 and centromere-associated DNA sequences in sugarcane. Chromosome Res 113:195–203CrossRefGoogle Scholar
  5. 5.
    Tek AL, Kashihara K, Murata M, Nagaki K (2011) Functional centromeres in Astragalus sinicus include a compact centromere-specific histone H3 and a 20-bp tandem repeat. Chromosome Res 19:969–978CrossRefPubMedGoogle Scholar
  6. 6.
    Neumann P, Navrátilová A, Schroeder-Reiter E, Koblížková A, Steinbauerová V, Chocholová E, Novák P, Wanner G, Macas J (2012) Stretching the rules: monocentric chromosomes with multiple centromere domains. PLoS Genet 8:e1002777CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Nagaki K, Yamamoto M, Yamaji N, Mukai Y, Murata M (2012) Chromosome dynamics visualized with an anti-centromeric histone H3 antibody in Allium. PLoS One 7:e51315CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Gong Z, Wu Y, Koblizkova A, Torres GA, Wang K, Iovene M, Neumann P, Zhang W, Novak P, Buell CR, Macas J, Jiang J (2012) Repeatless and repeat-based centromeres in potato: implications for centromere evolution. Plant Cell 24:3559–3574CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Nagaki K, Tanaka K, Yamaji N, Kobayashi H, Murata M (2015) Sunflower centromeres consist of a centromere-specific LINE and a chromosome-specific tandem repeat. Front Plant Sci 6:912CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Institute of Plant Science and ResourcesOkayama UniversityKurashikiJapan

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