An Efficient Chromatin Immunoprecipitation (ChIP) Protocol for Studying Histone Modifications in Arabidopsis Plants
Abstract
Chromatin immunoprecipitation (ChIP) is a powerful tool for the characterization of covalent histone modifications and DNA-histone interactions in vivo. The procedure includes DNA-histone cross-linking in chromatin, shearing DNA into smaller fragments, immunoprecipitation with antibodies against the histone modifications of interest, followed by PCR identification of associated DNA sequences. In this protocol, we describe a simplified and optimized version of ChIP assay by reducing the number of experimental steps and isolation solutions and shortening preparation times. We include a nuclear isolation step before chromatin shearing, which provides a good yield of high-quality DNA resulting in at least 15 mug of DNA from each immunoprecipitated sample (from 0.2 to 0.4 g of starting tissue material) sufficient to test > or =25 genes of interest. This simpler and cost-efficient protocol has been applied for histone-modification studies of various Arabidopsis thaliana tissues and is easy to adapt for other systems as well.
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This cost-effective and efficient ChIP protocol has been successfully applied to Arabidopsis thaliana and can be adapted to other systems for epigenetic research.
“This cost-effective and efficient protocol has been successfully applied to Arabidopsis thaliana and can be adapted to other systems for epigenetic research [150].”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [150]
In Arabidopsis, a ChIP method including nuclear isolation before chromatin shearing improved DNA yield (15 g from 0.2-0.4g of tissue), sufficient for analyzing 25 or more genes.
“In Arabidopsis, this method includes a nuclear isolation step before chromatin shearing, improving DNA yield (15 g from 0.2-0.4g of tissue), sufficient for analyzing 25 or more genes.”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [150]
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- Authors
- Saleh, A., Alvarez-Venegas, R., & Avramova, Z.
- Affiliations
- University of Nebraska–Lincoln (US)
- Corresponding author
- Saleh, Abdelaty
- Avramova, Zoya
- ORCID
- Avramova, Zoya
- Venue
- Nature Protocols
- Published
- 2008-05-22
- Volume
- 3
- Issue
- 6
- Pages
- 1018-1025
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- OpenAlex
- W2030132680
- Cited by
- 641
- References
- 41
- Citations by year
- 2026: 43 · 2025: 46 · 2024: 49 · 2023: 47 · 2022: 63 · 2021: 43 · 2020: 70 · 2019: 40 · 2018: 41 · 2017: 25 · 2016: 37 · 2015: 29 · 2014: 37 · 2013: 21 · 2012: 19
- FWCI
- 4.25
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Protocols (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Division of Molecular and Cellular Biosciences
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- chromatin immunoprecipitation, histone modifications, Arabidopsis thaliana, nuclear isolation, immunoprecipitation, histone-DNA interactions, plant epigenetics
- MeSH terms
- Histones, Arabidopsis, DNA, Plant, Arabidopsis Proteins, Epigenesis, Genetic, Chromatin Immunoprecipitation
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