Cited by 925Genomics and Chromatin DynamicsChromatin Remodeling and CancerEpigenetics and DNA Methylation

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Regulation of nucleosome dynamics by histone modifications

Zentner, Gabriel E, Henikoff, Steven·2013·Nature Structural & Molecular Biology

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Abstract

Chromatin is a dynamic structure that must respond to myriad stimuli to regulate access to DNA, and chemical modification of histones is a major means by which the cell modulates nucleosome mobility and turnover. Histone modifications are linked to essentially every cellular process requiring DNA access, including transcription, replication and repair. Here we consider properties of the major types of histone modification in the context of their associated biological processes to view them in light of the cellular mechanisms that regulate nucleosome dynamics.

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Bannister, A. J., Zegerman, P., Partridge, J. F., Miska, E. A., Thomas, J. O., Allshire, R. C., & Kouzarides, T. (2001) · Nature · doi:10.1038/35065138 · Cited by 2,903
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Paull, T. T., Rogakou, E. P., Yamazaki, V., Kirchgessner, C. U., Gellert, M., & Bonner, W. M. (2000) · Current Biology · doi:10.1016/s0960-9822(00)00610-2 · Cited by 2,098
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Uropathogenic Escherichia coli Virulence Factor α-Hemolysin Reduces Histone Acetylation to Inhibit Expression of Proinflammatory Cytokine Genes
Zhang, Z., Wang, M., Zhang, Y., Zhang, Y., Bartkuhn, M., Markmann, M., Hossain, H., Chakraborty, T., Hake, S. B., Jia, Z., et al. (2021) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiab018 · Cited by 11
Antisense-mediated repression of SAGA-dependent genes involves the HIR histone chaperone
Soudet, J., Beyrouthy, N., Pastucha, A., Maffioletti, A., Menéndez, D., Bakir, Z., & Stutz, F. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac264 · Cited by 8
“Hence, eukaryotic transcription units are organized into arrays with short linkers between two nucleosomes interspersed with Nucleosome Depleted Regions (NDRs) that constitute gene promoters (1,4-6).”
Background
ING4 and ING5 are essential for histone H3 lysine 14 acetylation and epicardial cell lineage development
Mah, S., Vanyai, H. K., Suen, C. S. N. L. W., Garnham, A. L., Wynn, J. E., Bergamasco, M., Malelang, S., Wilcox, S., Biben, C., Smyth, G. K., et al. (2024) · Development · doi:10.1242/dev.202617 · Cited by 8
Epigenetic regulation of the human genome: coherence between promoter activity and large-scale chromatin environment
Julienne, H., Zoufir, A., Audit, B., & Arnéodo, A. (2013) · Frontiers in Life Science · doi:10.1080/21553769.2013.832706 · Cited by 10
“…et al. 2012; Struhl & Segal 2013), the chromatin structure is subject to various epigenetic modifications in any given cell type, including DNA methylation, histone modifications, histone variant incorporation and DNA-binding proteins (Kouzarides 2007; Zhou et al. 2011; Zentner & Henikoff 2013).”
Background
DNA Methylation – Introduction
Neidhart, M. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-420194-1.00001-4 · Cited by 8
A role for Rtt109 in buffering gene-dosage imbalance during DNA replication
Voichek, Y., Bar‐Ziv, R., & Barkai, N. (2016) · Nucleus · doi:10.1080/19491034.2016.1216743 · Cited by 8
“This modification pattern, termed the ‘epigenetic landscape’ is shaped by chromatin modifiers that modify histones at specific positions both in preparation to processes such as gene transcription or DNA replication, or as a consequence of these same processes.(3) As such, histone modification provides a”
Background
Epigenetic Regulation of Adipokines
Pham, T. X., & Lee, J. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18081740 · Cited by 10
“The acetylation of lysine on histone tails neutralizes positive charge of lysine residues, which weakens charge-dependent histone–histone interactions and the interaction between histones and the negatively charged backbone of DNA [20].”
Dissection of structural dynamics of chromatin fibers by single-molecule magnetic tweezers
Xiao, X., Dong, L., Wang, Y., Wang, P., Li, M., Li, G., Chen, P., & Li, W. (2018) · Biophysics Reports · doi:10.1007/s41048-018-0064-0 · Cited by 8
Epigenomic signatures in age-related macular degeneration: Focus on their role as disease modifiers and therapeutic targets
Caputo, V., Strafella, C., Termine, A., Fabrizio, C., Ruffo, P., Cusumano, A., Giardina, E., Ricci, F., & Cascella, R. (2021) · European Journal of Ophthalmology · doi:10.1177/11206721211028054 · Cited by 8
Epigenetic Regulation in Heart Failure
DiSalvo, T. G. (2015) · Cardiology in Review · doi:10.1097/crd.0000000000000074 · Cited by 9
“Methylation of distal enhancer elements is often inversely correlated with their activity Partially methylated domains (<70% CpG methylation domains) become further hypomethylated in cancers and coincide with histone marks associated with transcriptional repression The family of TET enzymes can oxidize 5mC to 5hmC, wh…”
Drought Stress and Chromatin: An Epigenetic Perspective
Khan, A. A., & Zinta, G. (2016) · Springer eBooks · doi:10.1007/978-3-319-32423-4_21 · Cited by 8
Isx9 Regulates Calbindin D28K Expression in Pancreatic β Cells and Promotes β Cell Survival and Function
Pujol, J. B., Heikkilä, E., Savoia, C., Hajibeigi, A., Marchi, U. D., Battiprolu, P. K., Öz, O. K., & Dioum, E. M. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19092542 · Cited by 10
Interplay between epigenetics and metabolism controls cancer stem cell plasticity
Choi, J.-E., & Baek, I. (2024) · Frontiers in Epigenetics and Epigenomics · doi:10.3389/freae.2024.1424163 · Cited by 7
The Genetic Architecture of the Human Corpus Callosum and its Subregions
Bhatt, R. R., Gadewar, S. P., Shetty, A., Gari, I. B., Haddad, E., Javid, S., Ramesh, A., Nourollahimoghadam, E., Zhu, A. H., de Leeuw, C., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-64791-3 · Cited by 7
“Environmental and cohort-speci ﬁ c in ﬂ uences are likely to modulate these effects.”
Wheat genomics frontiers for gene discovery and breeding applications
Waqas, M., Rasheed, A., & Peng, J. (2025) · WheatOmics · doi:10.1007/s44412-025-00002-6 · Cited by 11
“Several types of PTMs modify the histone tails including acetylation, methylation, phosphorylation, sumoylation, glycosylation and carbonylation (Zentner and Henikoff 2013).”
The MMP-2 histone H3 N-terminal tail protease is selectively targeted to the transcription start sites of active genes
Weekley, B. H., & Rice, J. C. (2023) · Epigenetics & Chromatin · doi:10.1186/s13072-023-00491-w · Cited by 7
Insights from ENCODE on Missing Proteins: Why β-Defensin Expression Is Scarcely Detected
Yang, F., Zhang, Y., Xu, S., Kong, N., Zhou, Y., Ren, Z., Deng, Y., Lin, L., Ren, Y., Wang, Q., et al. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00565 · Cited by 7
Interdependency Between Genetic and Epigenetic Regulatory Defects in Cancer
Targa, F. R. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0856-1_4 · Cited by 6
Identification of novel Mendelian disorders of the epigenetic machinery (MDEMs)-associated functional mutations and neurodevelopmental disorders
Li, S., Li, H., Liu, D., Xing, Q., Chen, X., Zhang, H., Wen, J., Zhu, H., Liang, D., Li, Z., et al. (2023) · QJM · doi:10.1093/qjmed/hcad005 · Cited by 7
Omics Tools for the Genome-Wide Analysis of Methylation and Histone Modifications
Jiménez‐Chillarón, J. C., Díaz, R., & Ramon‐Krauel, M. (2014) · Comprehensive analytical chemistry · doi:10.1016/b978-0-444-62651-6.00004-0 · Cited by 7
Spt6
Kato, H., Okazaki, K., & Urano, T. (2013) · Epigenetics · doi:10.4161/epi.26487 · Cited by 7
“Positioning and posttranslational modifications of histones determine the state of chromatin in cis.(1,2) Of the three canonical RNA polymerases in eukaryotes, only RNA polymerase II (RNAP II) can transcribe nucleosome templates without changing nucleosome positioning in vitro.”
Epigenetic Mechanisms in Head and Neck Cancer
Osorio, J. C., & Castillo, A. (2016) · InTech eBooks · doi:10.5772/61135 · Cited by 7
“Histone lysine acetylation also functions in other cellular processes that require DNA access.[27]”
Background
Partial purification of histone H3 proteolytic activity from the budding yeast Saccharomyces cerevisiae
Azad, G. K., & Tomar, R. S. (2016) · Yeast · doi:10.1002/yea.3153 · Cited by 7
“The histone proteins are liable to various kinds of reversible post-translational modifications (PTMs), including acetylation, methylation, phosphorylation, ubiquitylation, biotinylation and sumoylation (Cuthbert et al., 2004; Kouzarides, 2007; Nelson et al., 2006; Strahl and Allis, 2000; Zentner and Henikoff, 2013).”
Background
Research Progress of Selective Small Molecule Bromodomain-Containing Protein 9 Inhibitors
Ma, H., Zhang, J., Zheng, P., Zhenwei, W., & Huibin, Z. (2018) · Future Medicinal Chemistry · doi:10.4155/fmc-2017-0243 · Cited by 7
G9a and G9a-Like Histone Methyltransferases and Their Effect on Cell Phenotype, Embryonic Development, and Human Disease
Eisenberg, C. A., & Eisenberg, L. M. (2019) · RNA technologies · doi:10.1007/978-3-030-14792-1_16 · Cited by 7
New molecular tumor markers for endometrial cancer.
Numa, F., Umayahara, K., Suehiro, Y., Suminami, Y., Oga, A., Sasaki, K., & Kato, H. (2001) · PubMed · Cited by 7
Refinement of bamboo genome annotations through integrative analyses of transcriptomic and epigenomic data
Ma, X., Zhao, H., Yan, H., Sheng, M., Cao, Y., Yang, K., Xu, H., Xu, W., Gao, Z., & Su, Z. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.04.068 · Cited by 7
“The dynamic structure of chromatin and various functions of genes rely on multiple epigenetic mechanisms, most notably post-translational modiﬁcation of histones [14,15].”
Background
Replication-coupled inheritance of chromatin states
Song, A., Wang, Y., Liu, C., Yu, J., Zhang, Z., Lan, L., Lin, H., Zhao, J., & Li, G. (2024) · Cell Insight · doi:10.1016/j.cellin.2024.100195 · Cited by 6
Epigenetics and Down syndrome
González-Molina, L. A., Dekker, A. D., Deyn, P. P. D., Dolga, A. M., & Rots, M. G. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-18516-8.00014-4 · Cited by 7
Modelling the conditional regulatory activity of methylated and bivalent promoters
Budden, D., Hurley, D., & Crampin, E. J. (2015) · Epigenetics & Chromatin · doi:10.1186/s13072-015-0013-9 · Cited by 6
“DNA replication [17, 18] or repair [19, 20]).”
PGC1α−1 Nucleosome Position and Splice Variant Expression and Cardiovascular Disease Risk in Overweight and Obese Individuals
Henagan, T. M., Stewart, L. K., Forney, L. A., Sparks, L. M., Johannsen, N. M., & Church, T. S. (2014) · PPAR Research · doi:10.1155/2014/895734 · Cited by 6

Authors: Zentner, G. E., & Henikoff, S.
Affiliations: Fred Hutch Cancer Center (US)
Howard Hughes Medical Institute (US)
Corresponding author: Henikoff, Steven
ORCID: Zentner, Gabriel E
Henikoff, Steven
Venue: Nature Structural & Molecular Biology
Publisher: Springer Science and Business Media LLC
Published: 2013-03
Volume: 20
Issue: 3
Pages: 259-266
ISSN: 1545-9985 (ISSN-L)
1545-9993
DOI: 10.1038/nsmb.2470
OpenAlex: W2034340491
Cited by: 923
References: 111
Citations by year: 2026: 22 · 2025: 33 · 2024: 57 · 2023: 39 · 2022: 45 · 2021: 60 · 2020: 63 · 2019: 82 · 2018: 75 · 2017: 84 · 2016: 76 · 2015: 106 · 2014: 125 · 2013: 52
FWCI: 11.25
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
Locations: Nature Structural & Molecular Biology (publishedVersion)
PubMed (publishedVersion)
Funders: Howard Hughes Medical Institute
National Institutes of Health (5u01hg004274-04)
National Human Genome Research Institute (5U01 HG004274)
National Cancer Institute (T32CA009657, U54CA143862)
National Institute of Environmental Health Sciences (R01ES020116)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords: nucleosome dynamics, histone modifications, chromatin, nucleosome mobility, nucleosome turnover, transcription, DNA replication, DNA repair
MeSH terms: Acetylation, Acylation, Adenosine Diphosphate, Chromatin, DNA, DNA Replication, Gene Expression Regulation, Glycosylation, Histones, Lysine, Methylation, Nucleosomes

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Regulation of nucleosome dynamics by histone modifications

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