Histone H3 globular domain acetylation identifies a new class of enhancers
Open accessAbstract
Histone acetylation is generally associated with active chromatin, but most studies have focused on the acetylation of histone tails. Various histone H3 and H4 tail acetylations mark the promoters of active genes. These modifications include acetylation of histone H3 at lysine 27 (H3K27ac), which blocks Polycomb-mediated trimethylation of H3K27 (H3K27me3). H3K27ac is also widely used to identify active enhancers, and the assumption has been that profiling H3K27ac is a comprehensive way of cataloguing the set of active enhancers in mammalian cell types. Here we show that acetylation of lysine residues in the globular domain of histone H3 (lysine 64 (H3K64ac) and lysine 122 (H3K122ac)) marks active gene promoters and also a subset of active enhancers. Moreover, we find a new class of active functional enhancers that is marked by H3K122ac but lacks H3K27ac. This work suggests that, to identify enhancers, a more comprehensive analysis of histone acetylation is required than has previously been considered.
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Enhancers devoid of the classic H3K27ac mark have been described.
“For example, enhancers devoid of the classic H3K27ac mark have recently been described [163]; consistent with this, it was shown that this mark is not required for enhancer function, at least in mouse ESCs [164].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [163]
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The Yin and Yang of Histone Marks in Transcription
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“Furthermore, focusing on accessible chromatin or common histone modifications to pinpoint enhancers, fails to identify enhancers lacking such common enhancer marks [36].”
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Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes
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Identification of the YEATS domain of GAS41 as a pH-dependent reader of histone succinylation
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Transcriptional enhancers and their communication with gene promoters
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“For example, enhancers devoid of the classic H3K27ac mark have recently been described [163]; consistent with this, it was shown that this mark is not required for enhancer function, at least in mouse ESCs [164].”
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“This potentially excludes other regions of the genome to be functionally assessed as they lack these associations but might nevertheless be functionally relevant (Pradeepa et al., 2016).”
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Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription
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“These four acetyl PTMs and H2AZ are associated with active transcription (Calo and Wysocka, 2013; Pradeepa et al., 2016), serve as potential anchors for BET proteins (Devaiah et al.”
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“The histone acetylation process is controlled by HATs and histone deacetylases (34).”
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“Thus, histone acetylation is in general functionally associated with gene activation [11].”
BackgroundEnhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma
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Causal role of histone acetylations in enhancer function
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“1), and it is important to consider the combinatorial features of enhancers to decipher the enhancer activity in a given cell type.(16,27)”
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KLF4 Nuclear Export Requires ERK Activation and Initiates Exit from Naive Pluripotency
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“Similarly, there are a number of binding sites for KLF4 andNANOGat enhancers downstream of Klf4, required for Klf4 transcription (Pradeepa et al., 2016; Sanchez-Castillo et al., 2014).”
BackgroundDynamic enhancers control skeletal muscle identity and reprogramming
Ramachandran, K., Senagolage, M. D., Sommars, M. A., Futtner, C. R., Omura, Y., Allred, A. L., & Barish, G. D. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000467 · Cited by 59 · see citing works
Metabolic intermediates – Cellular messengers talking to chromatin modifiers
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“In recent years, the role of acetylation within histone globular domain in regulation of transcription has also been reported [23,25,59].”
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Epigenetics and Inflammation in Diabetic Nephropathy
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“These modifications usually happen at promoters, insulators, enhancers, and other cis-regulatory regions, and finally lead to aberrant gene expression (Barski et al., 2007; Heintzman et al., 2009; Pradeepa et al., 2016).”
BackgroundKAP1 facilitates reinstatement of heterochromatin after DNA replication
Jang, S. M., Kauzlaric, A., Quivy, J., Pontis, J., Rauwel, B., Coluccio, A., Offner, S. E., Duc, J., Turelli, P., Almouzni, G., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky580 · Cited by 50 · see citing works
“Acetylation at this histone residue (H3K64ac) was recently reported to facilitate transcription (58) and to provide the underlying DNA with enhancer activity (59).”
BackgroundEpigenetics and microRNAs in cardiovascular diseases
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Acetylation of histone H3 in cancer progression and prognosis
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“Acetylation of lysine residues 64 and 122 in the globular domain of histone H3 (H3K64ac and H3K122ac, respectively) marks active gene promoters and also a subset of enhancers [98].”
BackgroundEpigenetics and its role in effecting agronomical traits
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“HATs activate genes by adding acetyl groups to lysine residues in histone N-terminal tails as well as globular domains (Bjerling et al., 2002; Pandey et al., 2002; Iwasaki et al., 2011; Pradeepa et al., 2016).”
BackgroundA hyperdynamic H3.3 nucleosome marks promoter regions in pluripotent embryonic stem cells
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“More recently, a new class of active functional enhancers, marked by H3K122ac, but which lack H3K27ac, was suggested to regulate a subset of developmental genes in mouse ESCs (47).”
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“Upon activation, enhancers transition to an open chromatin state and gain histone-specific acetylation, including the acetylation of H3 lysine 27 (H3K27ac) [22,23].”
BackgroundEpigenetic memory: A macrophage perspective
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“Within cellular chromatin, we can use generic technologies to systematically map accessible regions [136,149], nucleosome-borne epigenetic signals [130,150], post-replicational 5-cytosine methylation [151,152] as well as looping interactions between enhancers and promoters [17].”
Pioneer activity distinguishes activating from non‐activating SOX2 binding sites
Maresca, M., van den Brand, T., Li, H., Teunissen, H., Davies, J. O. J., & de Wit, E. (2023) · The EMBO Journal · doi:10.15252/embj.2022113150 · Cited by 35 · see citing works
Enhancer RNAs step forward: new insights into enhancer function
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Emerging Roles of Vitamin B12 in Aging and Inflammation
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Is There a Histone Code for Cellular Quiescence?
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Psip1/p52 regulates posterior Hoxa genes through activation of lncRNA Hottip
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The role and prospect of lysine‐specific demethylases in cancer chemoresistance
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“…and Lania, 1996; Groner et al., 2010), and its fusion to dCas9 results in 50%–99% gene repression in various cell lines, primary cultures, and pluripotent stem cells (Gao et al., 2013; Kearns et al., 2015; Shechner et al., 2015; THAKORE et al., 2015; Amabile et al., 2016; Pradeepa et al., 2016).”
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“pled at promoters compared with enhancers, perhaps reflecting the fact that not all active enhancers seem to require H3K27ac (Bonn et al. 2012; Pradeepa et al. 2016).”
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“In addition to these histone tail modifications, globular domain modifications such as H3K122ac have also been used to identify active enhancers that lack some classical marks of enhancer activity [21].”
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Role of Histone Acetylation and Acetyltransferases in Gene Regulation
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Self-citationCornelia de Lange syndrome-associated mutations cause a DNA damage signalling and repair defect
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Self-citationInducible CRISPRa screen identifies putative enhancers.
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“H3K4me1 and acetylation of specific lysine residues on histone H3 (H3K27ac, H3K64ac, H3K122ac) and H4 (H4K16ac) and, in some cases, eRNA transcription (Kim et al., 2010; Pradeepa et al., 2016; Shlyueva et al., 2014; Taylor et al., 2013).”
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4See: A Flexible Browser to Explore 4C Data
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“Notably, only one site (DDE3) displayed strongly significant H3K4me1 and H3K27ac peaks and this was only occupied by Tbxta and not by Tbx16 (Fig.”
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“Acetylation of H3K122 and H3K64 breaks the interaction between histone tails on adjacent nucleosomes and loosens the connection between nucleosomes (23).”
BackgroundResveratrol inhibits ACHN cells via regulation of histone acetylation
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“…and acetylation is an epigenetic mechanism that plays a very important role in RCC. Acetylation is one of the important epigenetic markers associated with histones and leads to chromatin remodelling and gene expression regulation in the enhancers and promoters of genes (Pradeepa et al. 2016).”
BackgroundTranscriptional enhancers: from prediction to functional assessment on a genome-wide scale
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“However, subclasses of active enhancers exist which lack the canonical H3K27ac profile and instead exhibit acetylation of histone H3 lysine 122 (H3K122ac) (Pradeepa et al. 2016).”
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“Global histone H3 acetylation marks a ready state of gene expression.(50,51) AF9 contains a YEATS domain in its N terminus, which recognizes H3 lysine acetylation, especially H3K9ac.”
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“2 that associates with gene transcription activities (Chen et al. 2013; Pradeepa et al. 2016; Smith et al. 2021; Bedi et al. 2022).”
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- Authors
- Pradeepa, M. M., Grimes, G. R., Kumar, Y., Olley, G., Taylor, G. C. A., Schneider, R., & Bickmore, W. A.
- Affiliations
- University of Essex (GB)
- Institute of Genetics and Cancer (GB)
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Pradeepa, Madapura M
- Bickmore, Wendy A
- ORCID
- Venue
- Nature Genetics
- Published
- 2016-04-18
- Volume
- 48
- Issue
- 6
- Pages
- 681-686
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC4886833
- OpenAlex
- W2342153705
- Cited by
- 240
- References
- 47
- Citations by year
- 2026: 19 · 2025: 22 · 2024: 18 · 2023: 22 · 2022: 22 · 2021: 24 · 2020: 36 · 2019: 27 · 2018: 21 · 2017: 21 · 2016: 7
- FWCI
- 13.17
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Open Access at Essex (University of Essex) (acceptedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- HAL (submittedVersion)
- Site cant be reached (submittedVersion)
- PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion)
- Queen Mary Research Online (Queen Mary University of London) (submittedVersion)
- Funders
- Agence Nationale de la Recherche
- Institut National de la Santé et de la Recherche Médicale
- Fondation pour la Recherche Médicale
- Medical Research Council
- FP7 Ideas: European Research Council (249956)
- 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
- histone acetylation, H3K27ac, enhancers, promoter, chromatin modification, embryonic stem cells, cancer cell lines, enhancer identification
- MeSH terms
- Acetylation, Enhancer Elements, Genetic, Gene Expression Regulation, Histones, Humans, Lysine, K562 Cells, Chromatin Immunoprecipitation, Embryonic Stem Cells
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