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Cited by 2,217Genomics and Chromatin DynamicsGenomics and Phylogenetic StudiesEpigenetics and DNA Methylation

ChIP–seq: advantages and challenges of a maturing technology

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Park, Peter J.·2009·Nature Reviews Genetics
DOI 10.1038/nrg2641PMC PMC3191340
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Abstract

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a technique for genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes. Owing to the tremendous progress in next-generation sequencing technology, ChIP-seq offers higher resolution, less noise and greater coverage than its array-based predecessor ChIP-chip. With the decreasing cost of sequencing, ChIP-seq has become an indispensable tool for studying gene regulation and epigenetic mechanisms. In this Review, I describe the benefits and challenges in harnessing this technique with an emphasis on issues related to experimental design and data analysis. ChIP-seq experiments generate large quantities of data, and effective computational analysis will be crucial for uncovering biological mechanisms.

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  • ChIP-seq is more costly than ChIP-chip but requires less DNA input.

    “Though ChIP-seq is more costly, it requires less DNA input (Park, 2009).”

    From The Epigenetics of Anxiety Pathophysiology: A DNA Methylation and Histone Modification Focused Review (2023) · cites this paper as Park, 2009

    The “Sample quantity” section says ChIP-seq needs less sample material than ChIP-chip and recommends 10–50 ng of ChIP DNA for the Illumina platform. The “Advantages and disadvantages” section calls cost a disadvantage, but says ChIP-seq is already less expensive than ChIP-chip for high-resolution profiling of an entire large genome. Thus, the unqualified claim that ChIP-seq is more costly overstates the source. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • Chromatin immunoprecipitation is capable of detecting and mapping protein-DNA interactions, including DNA-binding sites for transcription factors, chromatin modeling proteins such as DNMTs, and histone modifications.

    “Chromatin immunoprecipitation (ChIP) is capable of detecting and mapping protein–DNA interactions, such as DNA-binding sites for specific proteins. These proteins include transcription factors and other chromatin modeling proteins such as DNMTs, but most importantly, they include histone modifications/markings (Park, 2009).”

    From The Epigenetics of Anxiety Pathophysiology: A DNA Methylation and Histone Modification Focused Review (2023) · cites this paper as Park, 2009

    The Introduction describes ChIP as enriching DNA fragments bound by a specific protein or class of nucleosomes, and says ChIP–seq maps transcription-factor binding sites and histone modifications. Our copy does not identify DNMTs as an example, and it treats histone modifications as marks to profile, not as proteins that bind DNA. It also does not rank histone modifications as the most important target. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

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Authors
Park, P. J.
Affiliations
Harvard University (US)
Corresponding author
Park, Peter J.
ORCID
Park, Peter J.
Venue
Nature Reviews Genetics
Publisher
Springer Science and Business Media LLC
Published
2009-09-08
Volume
10
Issue
10
Pages
669-680
ISSN
  • 1471-0056 (ISSN-L)
  • 1471-0064
DOI
10.1038/nrg2641
PMC
PMC3191340
OpenAlex
W2171111703
Cited by
2,217
References
10
Citations by year
2026: 100 · 2025: 130 · 2024: 177 · 2023: 150 · 2022: 144 · 2021: 122 · 2020: 100 · 2019: 88 · 2018: 98 · 2017: 94 · 2016: 101 · 2015: 137 · 2014: 165 · 2013: 147 · 2012: 176
FWCI
11.79
Type
journal article
Language
en
Open access
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature Reviews Genetics (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Institutes of Health
  • National Human Genome Research Institute (U01HG004258)
  • National Institute of General Medical Sciences (R01GM082798)
  • National Institute of Dental and Craniofacial Research (RL1DE019021)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
ChIP-seq, chromatin immunoprecipitation, DNA-binding proteins, histone modifications, nucleosome mapping, gene expression regulation, epigenetics, ChIP-chip, next-generation sequencing, experimental design, data analysis, computational analysis
MeSH terms
Animals, DNA-Binding Proteins, Humans, Nucleosomes, Sequence Analysis, DNA, Computational Biology, Epigenesis, Genetic, Chromatin Immunoprecipitation

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