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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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“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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Is There a Histone Code for Cellular Quiescence?
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Psip1/p52 regulates posterior Hoxa genes through activation of lncRNA Hottip
Pradeepa, M. M., McKenna, F., Taylor, G. C. A., Bengani, H., Grimes, G. R., Wood, A. J., Bhatia, S., & Bickmore, W. A. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006677 · Cited by 32
Self-citationEpigenomic insights into common human disease pathology
Bell, C. G. (2024) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-024-05206-2 · Cited by 36
The role and prospect of lysine‐specific demethylases in cancer chemoresistance
Song, Y., Yang, G., Ma, D., Wang, W., & Leung, C. (2023) · Medicinal Research Reviews · doi:10.1002/med.21955 · Cited by 32
Overview of advances in CRISPR/deadCas9 technology and its applications in human diseases
Kanafi, M. M., & Tavallaei, M. (2022) · Gene · doi:10.1016/j.gene.2022.146518 · Cited by 37
Levy, S., Somasundaram, L., Raj, I. X., Ic-Mex, D., Phal, A., Schmidt, S., Ng, W. I., Mar, D., Decarreau, J. A., Moss, N., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110457 · Cited by 31
“…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).”
BackgroundFloc’hlay, S., Wong, E. S. W., Zhao, B., Viales, R. R., Thomas‐Chollier, M., Thieffry, D., Garfield, D. A., & Furlong, E. E. M. (2020) · Genome Research · doi:10.1101/gr.266338.120 · Cited by 30
“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).”
BackgroundWolfe, J. C., Mikheeva, L. A., Hagras, H., & Zabet, N. R. (2021) · Genome biology · doi:10.1186/s13059-021-02532-7 · Cited by 28
“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].”
Bedi, Y. S., Roach, A. N., Thomas, K. N., Mehta, N. A., & Golding, M. C. (2022) · Epigenetics & Chromatin · doi:10.1186/s13072-021-00433-4 · Cited by 31
Role of Histone Acetylation and Acetyltransferases in Gene Regulation
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Chromatin profiling of cortical neurons identifies individual epigenetic signatures in schizophrenia
Gusev, F. E., Reshetov, D. A., Mitchell, A., Андреева, Т. В., Dincer, A., Grigorenko, A. P., Fedonin, G. G., Halene, T. B., Aliseychik, M., Filippova, E., et al. (2019) · Translational Psychiatry · doi:10.1038/s41398-019-0596-1 · Cited by 24
Epigenetic regulation of intestinal stem cell differentiation
Verzi, M. P., & Shivdasani, R. A. (2020) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00084.2020 · Cited by 28
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Self-citationCornelia de Lange syndrome-associated mutations cause a DNA damage signalling and repair defect
Olley, G., Pradeepa, M. M., Grimes, G. R., Piquet, S., Polo, S. E., FitzPatrick, D. R., Bickmore, W. A., & Boumendil, C. (2021) · Nature Communications · doi:10.1038/s41467-021-23500-6 · Cited by 25
Self-citationInducible CRISPRa screen identifies putative enhancers
Dai, Z., Li, R., Hou, Y., Li, Q., Zhao, K., Li, T., Li, M. J., & Wu, X. (2021) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2021.06.012 · Cited by 25
PARP mediated chromatin unfolding is coupled to long-range enhancer activationPreprint
Benabdallah, N. S., Williamson, I., Illingworth, R. S., Boyle, S., Grimes, G. R., Therizols, P., & Bickmore, W. A. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/155325 · Cited by 24
“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).”
BackgroundSelf-citationMarques, D., Vaziri, N., Greenway, S. C., & Bousman, C. (2024) · Molecular Psychiatry · doi:10.1038/s41380-024-02735-x · Cited by 25
Establishment and function of chromatin modification at enhancers
Tafessu, A., & Banaszynski, L. A. (2020) · Open Biology · doi:10.1098/rsob.200255 · Cited by 24
Retrospective analysis of enhancer activity and transcriptome history
Boers, R., Boers, J., Tan, B. F., van Leeuwen, M. E., Wassenaar, E., Sanchez, E. G., Sleddens–Linkels, E., Tenhagen, Y., Mulugeta, E., Laven, J. S. E., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01683-1 · Cited by 25
Epigenetics of cutaneous T-cell lymphoma: biomarkers and therapeutic potentials
Lai, P., & Wang, Y. (2021) · Cancer Biology and Medicine · doi:10.20892/j.issn.2095-3941.2020.0216 · Cited by 25
4See: A Flexible Browser to Explore 4C Data
Zouari, Y. B., Platania, A., Molitor, A., & Sexton, T. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2019.01372 · Cited by 16
Armenta‐Castro, E., Reyes‐Vallejo, T., Máximo‐Sánchez, D., Camacho, I. H., López‐López, G., Reyes-Carmona, S. R., Conde‐Rodríguez, I., Ramírez‐Díaz, I., Aguilar‐Lemarroy, A., Jave‐Suárez, L. F., et al. (2020) · FEBS Open Bio · doi:10.1002/2211-5463.12973 · Cited by 22
Fgf-driven Tbx protein activities directly induce myf5 and myod to initiate zebrafish myogenesis
Osborn, D. P. S., Li, K., Cutty, S. J., Nelson, A. C., Wardle, F. C., Hinits, Y., & Hughes, S. M. (2020) · Development · doi:10.1242/dev.184689 · Cited by 21
“Notably, only one site (DDE3) displayed strongly significant H3K4me1 and H3K27ac peaks and this was only occupied by Tbxta and not by Tbx16 (Fig.”
BackgroundInfluentialTargeting Epigenetic Mechanisms in Vascular Aging
Lin, Z., Ding, Q., Li, X., Feng, Y., He, H., Huang, C., & Zhu, Y. Z. (2022) · Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2021.806988 · Cited by 23
“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
Dai, L., Chen, L., Wang, W., & Lin, P.-Z. (2020) · Pharmaceutical Biology · doi:10.1080/13880209.2020.1738503 · Cited by 20
“…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
Tobias, I. C., Abatti, L. E., Moorthy, S. D., Mullany, S., Taylor, T., Khader, N., Filice, M., & Mitchell, J. A. (2020) · Genome · doi:10.1139/gen-2020-0104 · Cited by 25
“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).”
BackgroundLiang, C., Niu, J., Wang, X., Zhang, Z., Yang, R., Yao, X., Liu, F., Li, W., Pei, S., Sun, H., et al. (2020) · Cancer Science · doi:10.1111/cas.14729 · Cited by 20
Tian, X., Yu, H. T., Li, D., Jin, G., Dai, S., Gong, P., Kong, C., & Wang, X. (2020) · Molecular Therapy · doi:10.1016/j.ymthe.2020.11.022 · Cited by 19
“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.”
BackgroundFuture in the past: paternal reprogramming of offspring phenotype and the epigenetic mechanisms
Wu, D., Zhang, K., Guan, K., Khan, F. A., Pandupuspitasari, N. S., Negara, W., Sun, F., & Huang, C. (2024) · Archives of Toxicology · doi:10.1007/s00204-024-03713-6 · Cited by 20
“2 that associates with gene transcription activities (Chen et al. 2013; Pradeepa et al. 2016; Smith et al. 2021; Bedi et al. 2022).”
Inge, M. M., Miller, R., Hook, H., Bray, D., Keenan, J. L., Zhao, R. W., Gilmore, T. D., & Siggers, T. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae706 · Cited by 18
Metadata
- 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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