Skip to main content

Chromatin Immunoprecipitation for Detecting Epigenetic Marks on Plant Nucleosomes

  • Protocol
  • First Online:
Chromosome and Genomic Engineering in Plants

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1469))

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  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 163:1221–1225

    CAS  PubMed  PubMed Central  Google Scholar 

  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 14:2825–2836

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 116:275–283

    Article  CAS  PubMed  Google Scholar 

  4. Nagaki K, Murata M (2005) Characterization of CENH3 and centromere-associated DNA sequences in sugarcane. Chromosome Res 113:195–203

    Article  Google Scholar 

  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 19:969–978

    Article  CAS  PubMed  Google Scholar 

  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:e1002777

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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:e51315

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 24:3559–3574

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 6:912

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Kiyotaka Nagaki .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Science+Business Media New York

About this protocol

Cite this protocol

Nagaki, K. (2016). Chromatin Immunoprecipitation for Detecting Epigenetic Marks on Plant Nucleosomes. In: Murata, M. (eds) Chromosome and Genomic Engineering in Plants. Methods in Molecular Biology, vol 1469. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-4931-1_16

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-4931-1_16

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-4929-8

  • Online ISBN: 978-1-4939-4931-1

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics