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Cited by 1,457Genomics and Chromatin DynamicsEpigenetics and DNA MethylationChromatin Remodeling and Cancer

Modification of Enhancer Chromatin: What, How, and Why?

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Calo, Eliezer, Wysocka, Joanna·2013·Molecular Cell
DOI 10.1016/j.molcel.2013.01.038PMC PMC3857148
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Abstract

Emergence of form and function during embryogenesis arises in large part through cell-type- and cell-state-specific variation in gene expression patterns, mediated by specialized cis-regulatory elements called enhancers. Recent large-scale epigenomic mapping revealed unexpected complexity and dynamics of enhancer utilization patterns, with 400,000 putative human enhancers annotated by the ENCODE project alone. These large-scale efforts were largely enabled through the understanding that enhancers share certain stereotypical chromatin features. However, an important question still lingers: what is the functional significance of enhancer chromatin modification? Here we give an overview of enhancer-associated modifications of histones and DNA and discuss enzymatic activities involved in their dynamic deposition and removal. We describe potential downstream effectors of these marks and propose models for exploring functions of chromatin modification in regulating enhancer activity during development.

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Crossref · 10.1016/j.molcel.2013.01.038

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  • H3K27ac at gene regulatory regions is dependent on the presence of H3K4me1, indicating H3K4me1 defines the future active enhancer.

    “The active histone modification H3K27ac at gene regulatory regions is dependent on the presence of H3K4me1, indicating H3K4me1 defines the future active enhancer30,34.”

    From HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements (2024) · cites this paper as [30]

    In “H3K4me1 at enhancers: a window of opportunity for enhancer deployment” (page not provided), the review says H3K27ac is acquired almost exclusively where H3K4me1 already exists. But it describes H3K4me1 as perhaps defining—or merely correlating with—a broad window for activation, not as determining which enhancers will become active. The claim overstates both dependence and predictive specificity. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Well-established enhancers bear biochemical marks that are routinely used to classify other sequences as enhancers, including sequence-level features, 1D biochemical annotations, direct binding of TFs or cofactors, and 3D biochemical annotations.

    “Well-established enhancers bear biochemical marks that are now routinely used to classify other sequences as enhancers. These include: sequence-level features (TF binding site motifs and conservation); 1D biochemical annotations (accessible chromatin; H3K27Ac and H3K4me1 modifications on flanking histones for active enhancers; H3K4me1 and HK27me3 for poised enhancers; closed chromatin that has”

    From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [103]

    The Introduction describes clustered TF recognition sites, and “Brief overview of enhancer chromatin features” says accessibility, H3K4me1, H3K27ac and coactivator occupancy are used to annotate enhancers. The Introduction also discusses 3D enhancer–promoter contacts, but the retrieved passage does not say those contacts are routinely used to classify sequences as enhancers; nor does the copy establish conservation as a routinely used feature. Page numbers are unavailable in our copy. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • H3K4me1 in combination with H3K27ac designates the active enhancer state, while H3K4me1 alone, or with H3K27me3, defines a primed or repressed enhancer, respectively.

    “Monomethylation on H3K4 (H3K4me1) in combination with acetylation of H3 at K27 (H3K27ac) designates the active enhancer state33 while H3K4me1 alone, or with trimethylation of H3K27 (H3K27me3), defines a primed or repressed enhancer, respectively30.”

    From HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements (2024) · cites this paper as [30]

  • Active and primed enhancers are marked by H3K4me1 in a cell type-specific manner.

    “In mammalian cells, active and primed enhancers are marked by monomethylation of histone 3 (H3) at lysine 4 (K4) (H3K4me1) in a cell type-specific manner.”

    From HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements (2024) · cites this paper as [30]

  • H3K27ac is associated with the active state of both enhancers and promoters.

    “In addition, acetylation of lysine 27 of histone 3 (H3K27ac) is associated with the active state of both elements.”

    From Hepatocyte Nuclear Factor 4‐Alpha Is Essential for the Active Epigenetic State at Enhancers in Mouse Liver (2019) · cites this paper as [14]

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Authors
Calo, E., & Wysocka, J.
Affiliations
Stanford Medicine (US)
Corresponding author
Wysocka, Joanna
ORCID
Venue
Molecular Cell
Publisher
Elsevier BV
Published
2013-03
Volume
49
Issue
5
Pages
825-837
ISSN
1097-2765 (ISSN-L)
DOI
10.1016/j.molcel.2013.01.038
PMC
PMC3857148
OpenAlex
W1986586739
Cited by
1,457
References
21
Citations by year
2026: 54 · 2025: 99 · 2024: 119 · 2023: 131 · 2022: 124 · 2021: 150 · 2020: 116 · 2019: 156 · 2018: 130 · 2017: 109 · 2016: 88 · 2015: 82 · 2014: 74 · 2013: 24
FWCI
8.39
Type
journal article
Language
en
Open access
Licence
Locations
  • Molecular Cell (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • Howard Hughes Medical Institute
  • W. M. Keck Foundation
  • Helen Hay Whitney Foundation
  • National Institute of General Medical Sciences (GM 095555-01, R01GM095555)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Keywords
enhancers, histone modifications, DNA modification, cis-regulatory elements, embryonic development, cell type-specific gene expression, developmental gene regulation
MeSH terms
Animals, Chromatin, Enhancer Elements, Genetic, Histones, Humans, Promoter Regions, Genetic, Epigenomics

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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