The DOI matches its Crossref record; 110 of the 111 references it cites were found in a registry or an index.
Regulation of nucleosome dynamics by histone modifications
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.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“histones enter in nucleosome formation and proper DNA wrapping after the S phase of cell cycle [65]”
Citations
Cites
Chromatin modifications and their function
Kouzarides, T. (2007) · Cell · doi:10.1016/j.cell.2007.02.005 · Cited by 10,883
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129
Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain
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
Mapping and analysis of chromatin state dynamics in nine human cell types
Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature · doi:10.1038/nature09906 · Cited by 2,898
ACETYLATION AND METHYLATION OF HISTONES AND THEIR POSSIBLE ROLE IN THE REGULATION OF RNA SYNTHESIS
Allfrey, V. G., Faulkner, R. D., & Mirsky, A. E. (1964) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.51.5.786 · Cited by 2,788
Combinatorial patterns of histone acetylations and methylations in the human genome
Wang, Z., Zang, C., Rosenfeld, J. A., Schones, D. E., Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Peng, W., Zhang, M. Q., et al. (2008) · Nature Genetics · doi:10.1038/ng.154 · Cited by 2,331
A unique chromatin signature uncovers early developmental enhancers in humans
Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233
A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage
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
DNA Replication in Eukaryotic Cells
Bell, S. P., & Dutta, A. (2002) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.71.110601.135425 · Cited by 2,065
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
Wang, K., Yang, Y. W., Liu, B., Sanyal, A., Corces, M. R., Chen, Y., Lajoie, B. R., Protacio, A., Flynn, R. A., Gupta, R. A., et al. (2011) · Nature · doi:10.1038/nature09819 · Cited by 2,005
Flagged first, then by citations
1 of the 111 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Regulation of type I interferon responses
Ivashkiv, L. B., & Donlin, L. T. (2013) · Nature reviews. Immunology · doi:10.1038/nri3581 · Cited by 3,442
Lämke, J., & Bäurle, I. (2017) · Genome biology · doi:10.1186/s13059-017-1263-6 · Cited by 954
“org/publicdomain/ze The structure of chromatin regulates the accessibility of genes for the transcriptional machinery, and is thus an integral part of regulated gene expression in stress responses and development [8, 9].”
BackgroundGetting up to speed with transcription elongation by RNA polymerase II
Jonkers, I., & Lis, J. T. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3953 · Cited by 876
Understanding nucleosome dynamics and their links to gene expression and DNA replication
Lai, W. K. M., & Pugh, B. F. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.47 · Cited by 495
Lämke, J., Brzezinka, K., Altmann, S., & Bäurle, I. (2015) · The EMBO Journal · doi:10.15252/embj.201592593 · Cited by 452
“For example, histone acetylation is associated with active transcription and correlates closely with the rate of transcription (Zentner & Henikoff, 2013).”
Release and activity of histone in diseases
Chen, R., Kang, R., Fan, X.-G., & Tang, D. (2014) · Cell Death and Disease · doi:10.1038/cddis.2014.337 · Cited by 436
“Moreover, histone post-translational modifications (PTMs) have a critical role in the regulation of nucleosome dynamics and multiple DNA-associated processes such as transcription, replication, and repair.(2,3) Various histone PTMs and their combinations lead to the generation of the histone code hypothesis and epigen…”
BackgroundTargeting histone methyltransferases and demethylases in clinical trials for cancer therapy
Morera, L., Lübbert, M., & Jung, M. (2016) · Clinical Epigenetics · doi:10.1186/s13148-016-0223-4 · Cited by 412
“A wide range of PTMs occurs not only at the histone N-terminal tails, including acetylation, methylation, phosphorylation, ubiquitination, SUMOylation, crotonylation, and others [12] but also in the core of the histones and in the C-terminal regions [13, 14].”
BackgroundNucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase
Weber, C. M., Ramachandran, S., & Henikoff, S. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.02.014 · Cited by 418
“Z and/or histone modifications enriched on the +1 and +2 nucleosomes (Zentner and Henikoff, 2013) account for the closer resemblance of RNAPII transit at gene body nucleosomes to its action on unmodified canonical nucleosomes in vitro.”
BackgroundSelf-citationPi, L., Aichinger, E., van der Graaff, E., Llavata‐Peris, C. I., Weijers, D., Hennig, L., Groot, E. P., & Laux, T. (2015) · Developmental Cell · doi:10.1016/j.devcel.2015.04.024 · Cited by 380
Mitochondria and Epigenetics – Crosstalk in Homeostasis and Stress
Matilainen, O., Quirós, P. M., & Auwerx, J. H. (2017) · Trends in Cell Biology · doi:10.1016/j.tcb.2017.02.004 · Cited by 376
The role of extracellular histone in organ injury
Silk, E., Zhao, H., Weng, H., & Ma, D. (2017) · Cell Death and Disease · doi:10.1038/cddis.2017.52 · Cited by 338
Chromatin and nucleosome dynamics in DNA damage and repairPreprint
Hauer, M., & Gasser, S. M. (2017) · Genes & Development · doi:10.1101/gad.307702.117 · Cited by 320
Inside HDACs with more selective HDAC inhibitors
Roche, J., & Bertrand, P. (2016) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2016.05.047 · Cited by 327
“[88] have identified by screening N-[1,3,4]thiadiazol-2-yl an d N-thiazol-2yl sulfonamide groups as promising ZBG, with probabl y etter physicochemical properties than hydroxamic acids as demonstrated by their current clinical applications .”
BackgroundWhat are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory
Steffen, P. A., & Ringrose, L. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3789 · Cited by 338
Roychowdhury, R., Das, S. P., Gupta, A., Parihar, P., Chandrasekhar, K., Sarker, U., Kumar, A., Ramrao, D. P., & Sudhakar, C. (2023) · Genes · doi:10.3390/genes14061281 · Cited by 333
Tatone, C., Emidio, G. D., Barbonetti, A., Carta, G., Luciano, A. M., Falone, S., & Amicarelli, F. (2018) · Human Reproduction Update · doi:10.1093/humupd/dmy003 · Cited by 296
Chromatin replication and epigenetic cell memory
Stewart-Morgan, K. R., Petryk, N., & Groth, A. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-0487-y · Cited by 290
Transgenerational developmental programming
Aiken, C., & Ozanne, S. E. (2013) · Human Reproduction Update · doi:10.1093/humupd/dmt043 · Cited by 295
“A number of possible modifications to histones are possible, including methylation, phosphorylation and acetylation, all of which can change the interaction between histones and DNA to alter gene expression (Zentner and Henikoff, 2013).”
BackgroundEpigenetics and Allergy: from Basic Mechanisms to Clinical Applications
Potaczek, D. P., Harb, H., Michel, S., Alhamwe, B. A., Renz, H. E., & Tost, J. (2017) · Epigenomics · doi:10.2217/epi-2016-0162 · Cited by 286
Mozzetta, C., Pontis, J., Fritsch, L., Robin, P., Portoso, M., Proux, C., Margueron, R., & Ait‐Si‐Ali, S. (2014) · Molecular Cell · doi:10.1016/j.molcel.2013.12.005 · Cited by 288
“Amino-terminal tails of core histones protrude from the nucleosome and are subject to a plethora of posttranslational modifications (PTMs), which regulate almost all cellular processes requiring access to DNA, in particular gene transcription (Zentner and Henikoff, 2013).”
BackgroundTargeting Metalloenzymes for Therapeutic Intervention
Chen, A. Y., Adamek, R. N., Dick, B. L., Credille, C. V., Morrison, C. N., & Cohen, S. M. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00201 · Cited by 284
Li, S., Lin, Y. J., Wang, P., Zhang, B., Li, M., Chen, S., Shi, R., Tunlaya‐Anukit, S., Liu, X., Wang, Z., et al. (2018) · The Plant Cell · doi:10.1105/tpc.18.00437 · Cited by 275
“…promoters with differential H3K9ac for both D5/ND and D7/ND was the ABRE consensus motif for the AREB1 TF. Charron et al., 2009; Zhou et al., 2010; Li et al., 2011; Zentner and Henikoff, 2013), combinations showing hUP-gUP and hDN-gDN are most likely to represent direct effects on gene expression.”
BackgroundJacquet, K., Fradet‐Turcotte, A., Avvakumov, N., Lambert, J., Lopez‐Roques, C., PANDITA, R. K., Paquet, É. R., Herst, P. M., Gingras, A., Pandita, T. K., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.03.031 · Cited by 280
“Histone post-translational modifications (PTMs) act as key regulators of chromatin organization, mainly by serving as docking sites for chromatin-binding factors (Zentner and Henikoff, 2013).”
BackgroundXavier, M. J., Roman, S. D., Aitken, R. J., & Nixon, B. (2019) · Human Reproduction Update · doi:10.1093/humupd/dmz017 · Cited by 272
Chromatin dynamics: Interplay between remodeling enzymes and histone modifications
Swygert, S. G., & Peterson, C. L. (2014) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2014.02.013 · Cited by 275
“Common modifications include lysine acetylation, the mono-, di-, or trimethylation of lysines, mono- or di-methylation of arginines, the phosphorylation of serines, threonines, or tyrosines, as well as lysine ubiquitylation and SUMOylation [6].”
BackgroundMethodInfluentialEZH2-Targeted Therapies in Cancer: Hype or a Reality
Eich, M., Athar, M., Ferguson, J. E., & Varambally, S. (2020) · Cancer Research · doi:10.1158/0008-5472.can-20-2147 · Cited by 254
“These enzymes catalyze a variety of posttranslational modifications including methylation, acetylation, phosphorylation, ubiquitination, and sumoylation (12).”
BackgroundBromodomains: Structure, function and pharmacology of inhibition
Ferri, E., Petosa, C., & McKenna, C. E. (2015) · Biochemical Pharmacology · doi:10.1016/j.bcp.2015.12.005 · Cited by 249
Narita, T., Ito, S., Higashijima, Y., Chu, W. K., Neumann, K., Walter, J., Satpathy, S., Liebner, T., Hamilton, W. B., Maskey, E., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.03.008 · Cited by 228
Wilkinson, J. L., Hooda, P. S., Barker, J., Barton, S., & Swinden, J. (2015) · Critical Reviews in Environmental Science and Technology · doi:10.1080/10643389.2015.1096876 · Cited by 235
“Zentner and Henikoff (2013) suggested histone modifications such as methylation, phosphorylation and acetylation can alter DNA access in such a way that that affects transcription, replication and repair.”
BackgroundA Macrohistone Variant Links Dynamic Chromatin Compaction to BRCA1-Dependent Genome Maintenance
Khurana, S., Kruhlak, M. J., Kim, J., Tran, A. D., Liu, J., Nyswaner, K., Shi, L., Jailwala, P., Sung, M.-H., Hakim, O., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.07.024 · Cited by 220
“Chromatin reorganization generally involves the covalent modification of histone tails as well as histone (variant) exchange, which together affect nucleosome density and DNA accessibility (Zentner and Henikoff, 2013).”
BackgroundRamazi, S., Allahverdi, A., & Zahiri, J. (2020) · Journal of Biosciences · doi:10.1007/s12038-020-00099-2 · Cited by 226
“This modification is known as one of the reversible types of PTMs in core histones and as well as linker histone H1 (Burzio et al. 1979; Messner and Hottiger 2011; van der Heden et al. 2010; Zentner and Henikoff 2013).”
BackgroundInfluentialUndercover: gene control by metabolites and metabolic enzymesPreprint
van der Knaap, J. A., & Verrijzer, C. P. (2016) · Genes & Development · doi:10.1101/gad.289140.116 · Cited by 222
“Transcriptional activity is intimately associated with specific histone modifications (Patel and Wang 2013; Zentner and Henikoff 2013; Swygert and Peterson 2014; Allis and Jenuwein 2016).”
BackgroundArabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling
Brzezinka, K., Altmann, S., Czesnick, H., Nicolas, P., Górka, M., Benke, E., Kabelitz, T., Jähne, F., Graf, A., Kappel, C., et al. (2016) · eLife · doi:10.7554/elife.17061 · Cited by 206
Zhou, H.-L., Luo, G., Wise, J. A., & Lou, H. J. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt875 · Cited by 211
“Intriguingly, in addition to methylation and acetylation, histones can be modified by the addition of other chemical moieties including phosphorylation, ubiquitination, sumoylation and ADP-ribosylation (116).”
BackgroundAlternative Splicing and Protein Diversity: Plants Versus Animals
Chaudhary, S., Khokhar, W., Jabre, I., Reddy, A. S. N., Byrne, L. J., Wilson, C. M., & Syed, N. H. (2019) · Frontiers in Plant Science · doi:10.3389/fpls.2019.00708 · Cited by 209
Targeting histone lysine demethylases — Progress, challenges, and the future
Thinnes, C. C., England, K. S., Kawamura, A., Chowdhury, R., Schofield, C. J., & Hopkinson, R. J. (2014) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2014.05.009 · Cited by 198
“These modifications, together with other factors, are proposed to substantially contribute to the regulation of gene expression in a context-dependent manner, in part by affecting the accessibility of DNAsequences for transcription [1–3].”
BackgroundDangerous liaisons: interplay between SWI/SNF, NuRD, and Polycomb in chromatin regulation and cancerPreprint
Bracken, A. P., Brien, G. L., & Verrijzer, C. P. (2019) · Genes & Development · doi:10.1101/gad.326066.119 · Cited by 203
“In addition, chromatin state is regulated through a plethora of posttranslationalmodifications, in particular of the unstructured N-terminal histone tails that protrude from the nucleosome (Zentner and Henikoff 2013; Allis and Jenuwein 2016).”
BackgroundTargeting histone lysine methylation in cancer
McGrath, J. P., & Trojer, P. (2015) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2015.01.002 · Cited by 190
Establishment and Functions of DNA Methylation in the Germline
Stewart-Morgan, K. R., Veselovska, L., & Kelsey, G. (2016) · Epigenomics · doi:10.2217/epi-2016-0056 · Cited by 195
Arif, K. M. T., Elliott, E. K., Haupt, L. M., & Griffiths, L. R. (2020) · Cancers · doi:10.3390/cancers12102922 · Cited by 201
Mechanosensing and Mechanoregulation of Endothelial Cell Functions
Fang, Y. H., Wu, D., & Birukov, K. G. (2019) · Comprehensive physiology · doi:10.1002/cphy.c180020 · Cited by 222
“Histone tail modifications influence nucleosome dynamics and chromatin compaction and control the activation or inactivation of nearby genes by determining the cis-DNA accessibility to chromatin remodeling complexes, transcription factors, and transcriptional coactivators/cosuppressors (435).”
Glutarylation of Histone H4 Lysine 91 Regulates Chromatin Dynamics
Bao, X., Liu, Z., Zhang, W., Gladysz, K., Fung, Y. M. E., Tian, G., Xiong, Y., Wong, J. W. H., Yuen, K. W. Y., & Li, X. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.08.018 · Cited by 171
Epigenetics in Insects: Genome Regulation and the Generation of Phenotypic Diversity
Glastad, K. M., Hunt, B. G., & Goodisman, M. A. D. (2018) · Annual Review of Entomology · doi:10.1146/annurev-ento-011118-111914 · Cited by 176
“This increases the accessibility of underlying DNA or facilitates the movement of the nucleosome along the DNA, both of which allow for the binding of DNA-binding factors (36, 150, 151).”
BackgroundLocal Determinants of the Mutational Landscape of the Human Genome
González-Pérez, A., Sabarinathan, R., & López-Bigas, N. (2019) · Cell · doi:10.1016/j.cell.2019.02.051 · Cited by 172
Mendelian Disorders of the Epigenetic Machinery: Tipping the Balance of Chromatin States
Fahrner, J. A., & Bjornsson, H. T. (2014) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090613-094245 · Cited by 166
“In general, acetylation of histones by histone acetyltransferases is associated with active gene expression, and deacetylated histones (mediated by histone deacetylases) tend to be present in transcriptionally silent regions (137).”
InfluentialIL-21 induces IL-22 production in CD4+ T cells
Yeste, A., Mascanfroni, I. D., Nadeau, M., Burns, E. J., Tukpah, A.-M. C., Santiago, A. F., Wu, C., Patel, B., Kumar, D., & Quintana, F. J. (2014) · Nature Communications · doi:10.1038/ncomms4753 · Cited by 159
Lewis, L. A., Polański, K., Zabala, M. D. T., Jayaraman, S., Bowden, L., Moore, J. D., Penfold, C. A., Jenkins, D. J., Hill, C., Baxter, L. A., et al. (2015) · The Plant Cell · doi:10.1105/tpc.15.00471 · Cited by 158
Molecular mechanisms of plant tolerance to heat stress: current landscape and future perspectives
Haider, S., Iqbal, J., Naseer, S., Yaseen, T., Shaukat, M., Bibi, H., Ahmad, Y., Daud, H., Abbasi, N. L., & Mahmood, T. (2021) · Plant Cell Reports · doi:10.1007/s00299-021-02696-3 · Cited by 159
“The chromatin structure and dynamics regulate gene expression by controlling the accessibility of genomic DNA sequence for the general transcriptional machinery, in response to development and stress event (Struhl and Segal 2013; Zentner and Henikoff 2013).”
BackgroundOncometabolites‐driven tumorigenesis: From genetics to targeted therapy
Morin, A., Letouzé, É., Gimenez‐Roqueplo, A., & Favier, J. (2014) · International Journal of Cancer · doi:10.1002/ijc.29080 · Cited by 162
Morrison, E. A., Bowerman, S., Sylvers-Davie, K. L., Wereszczynski, J., & Musselman, C. A. (2018) · eLife · doi:10.7554/elife.31481 · Cited by 148
“The titration of DNA-bound H3(1-10)K4me3 into (15)N382 PHD yielded very similar CSPs as were observed upon titration of H3(1-10)K4me3 383 alone (Figure 6A).”
InfluentialRoles of Histone Deacetylases and Inhibitors in Anticancer Therapy
Verza, F. A., Das, U., Fachin, A. L., Dimmock, J. R., & Marins, M. (2020) · Cancers · doi:10.3390/cancers12061664 · Cited by 149
“This weakened binding can facilitate the action of transcription factors in this altered region, inducing or repressing gene transcription [13].”
BackgroundHuang, H., Nace, G., McDonald, K.-A., Tai, S., Klune, J. R., Rosborough, B. R., Ding, Q., Loughran, P., Zhu, X., Beer–Stolz, D., et al. (2013) · Hepatology · doi:10.1002/hep.26976 · Cited by 148
“X has been shown to be phosphorylated in response to DNA damage, serving as a marker of DNA damage.(18) We found that loss of HMGB1 within hepatocytes resulted in a”
BackgroundGaarenstroom, T., & Hill, C. S. (2014) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2014.01.009 · Cited by 151
“High hisone turnover in combination with the neutralization of positive harge resulting from the acetylation, likely aid in the creation of ore accessible chromatin [8,9].”
BackgroundStress memory responses and seed priming correlate with drought tolerance in plants: an overview
Liu, X., Quan, W., & Bartels, D. (2022) · Planta · doi:10.1007/s00425-022-03828-z · Cited by 148
“Histone methylation predominantly occurs on lysine and arginine residues including mono-methylation, di-methylation, or tri-methylation (Bannister and Kouzarides 2011; Zentner and Henikoff 2013).”
BackgroundZhong, H.-J., Lu, L., Leung, K.-H., Wong, C. C. L., Peng, C., Yan, S.-C., Ma, D.-L., Cai, Z., David Wang, H.-M., & Leung, C.-H. (2015) · Chemical Science · doi:10.1039/c5sc02321a · Cited by 138
Glucocorticoids, genes and brain function
Juszczak, G. R., & Stankiewicz, A. M. (2017) · Progress in Neuro-Psychopharmacology and Biological Psychiatry · doi:10.1016/j.pnpbp.2017.11.020 · Cited by 138
Histone Lysine and Genomic Targets of Histone Acetyltransferases in Mammals
Voss, A. K., & Thomas, T. (2018) · BioEssays · doi:10.1002/bies.201800078 · Cited by 141
Hiragami-Hamada, K., Soeroes, S., Nikolov, M., Wilkins, B. J., Kreuz, S., Chen, C. C. L., Rosa-Velázquez, I. A. D. L., Zenn, H.-M., Kost, N., Pohl, W. H., et al. (2016) · Nature Communications · doi:10.1038/ncomms11310 · Cited by 145
Keeping it quiet: chromatin control of gammaherpesvirus latency
Lieberman, P. M. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro3135 · Cited by 139
Epigenetic control of gene regulation during development and disease: A view from the retina
Corso‐Díaz, X., Jaeger, C., Chaitankar, V., & Swaroop, A. (2018) · Progress in Retinal and Eye Research · doi:10.1016/j.preteyeres.2018.03.002 · Cited by 130
“Due to their impact on chromatin structure and DNA accessibility, histones are key regulators of all major chromatin-related processes, including DNA transcription, replication and repair (Zentner and Henikoff, 2013).”
BackgroundHigh-resolution digital profiling of the epigenome
Zentner, G. E., & Henikoff, S. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3798 · Cited by 127
“…layer of regulatory information superimposed on the genome and includes nucleosome occupancy 1 , positioning 1 , composition 2 , modification 3 and dynamics 4 , as well as DNA methylation 5 ; it is shaped by the action of transcription factors (TFs) 6 , ATP-dependent chromatin remodellers 7…”
Self-citationSeuter, S., Neme, A., & Carlberg, C. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1519 · Cited by 128
“Epigenomic effects are assumed to be mediated primarily by chromatin modifying enzymes that act quickly (45).”
BackgroundBromodomains and Their Pharmacological Inhibitors
Gallenkamp, D., Gelato, K. A., Haendler, B., & Weinmann, H. (2014) · ChemMedChem · doi:10.1002/cmdc.201300434 · Cited by 129
ISWI chromatin remodeling complexes in the DNA damage response
Aydın, Ö. Z., Vermeulen, W., & Lans, H. (2014) · Cell Cycle · doi:10.4161/15384101.2014.956551 · Cited by 125
“This in turn may lead to the modulation of nucleosome dynamics by altering histone-DNA contacts or to the chromatin association of proteins that act on DNA or mediate signaling responses.(7) Many different types of histone modifications play essential roles in orchestrating DNA repair and DNA damage signaling, includi…”
BackgroundEmerging Roles for Polycomb-Group Proteins in Stem Cells and Cancer
Chan, H. L., & Morey, L. (2019) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2019.04.005 · Cited by 131
Wong, C. P., Hsu, A., Buchanan, A., Palomera‐Sánchez, Z., Beaver, L. M., Houseman, E. A., Williams, D. E., Dashwood, R. H., & Ho, E. (2014) · PLoS ONE · doi:10.1371/journal.pone.0086787 · Cited by 125
Histone Tail Conformations: A Fuzzy Affair with DNA
Ghoneim, M., Fuchs, H. A., & Musselman, C. A. (2021) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2020.12.012 · Cited by 132
Ibeagha-Awemu, E. M., & Zhao, X. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00302 · Cited by 134
“The nucleosome is an octamer of four histones (H2A, H2B, H3, and H4) densely packed to achieve a fold compaction necessary to fit a genome into the nucleus while also allowing enough room for proteins involved in transcription, replication, and repair to access DNA (Zentner and Henikoff, 2013).”
BackgroundJha, D. K., & Strahl, B. D. (2014) · Nature Communications · doi:10.1038/ncomms4965 · Cited by 123
Super enhancer regulation of cytokine-induced chemokine production in alcoholic hepatitis
Liu, M., Cao, S., He, L., Gao, J., Arab, J. P., Cui, H., Xuan, W., Gao, Y., Sehrawat, T. S., Hamdan, F. H., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24843-w · Cited by 120
Kim, K., Punj, V., Kim, J., Lee, S., Ulmer, T. S., Lu, W., Rice, J. C., & An, W. (2016) · Genes & Development · doi:10.1101/gad.268714.115 · Cited by 120
“This is exemplified by the various covalent post-translational modifications (PTMs) of the N-terminal tails (NTs) of the core histone proteins (H3, H4, H2A, and H2B) that alter nucleosome composition to regulate fundamental DNA-templated programs such as transcription (Zentner and Henikoff 2013).”
BackgroundFunctions and mechanisms of plant histone deacetylases
Chen, X., Ding, A. B., & Zhong, X. (2019) · Science China Life Sciences · doi:10.1007/s11427-019-1587-x · Cited by 119
Update on epigenetics in allergic disease
Harb, H., & Renz, H. (2015) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2014.11.009 · Cited by 115
Cortini, R., Barbi, M., Caré, B. R., Lavelle, C., Lesne, A., Mozziconacci, J., & Victor, J. (2016) · Reviews of Modern Physics · doi:10.1103/revmodphys.88.025002 · Cited by 116
“The repertory of histone-tail PTMs is vast both in terms of types of modifications and in terms of where the modification can take place (Zentner and Henikoff, 2013; Fierz, 2014; Pepenella, Murphy, and Hayes, 2014).”
BackgroundBerry, S. M., Dean, C., & Howard, M. (2017) · Cell Systems · doi:10.1016/j.cels.2017.02.013 · Cited by 112
“This effect may be due to a more compact chromatin structure and lower levels of histone acetylation at repressed genes, which tends to promote retention of histones (reviewed in (Zentner and Henikoff, 2013)).”
Damage-associated molecular patterns (DAMPs) in diseases: implications for therapy
Lin, H., Xiong, W. G., Fu, L., Yi, J., & Yang, J. (2025) · Molecular Biomedicine · doi:10.1186/s43556-025-00305-3 · Cited by 137
Endocrine disruption of the epigenome: a breast cancer link
Knower, K. C., To, S. Q., Leung, Y., Ho, S., & Clyne, C. D. (2014) · Endocrine Related Cancer · doi:10.1530/erc-13-0513 · Cited by 109
“Lysine residues may be mono-, di- or trimethylated, although this is thought to have a less direct effect on chromatin dynamics due to the nil effect this has on overall histone charge (Zentner & Henikoff 2013).”
BackgroundLocato, V., Cimini, S., & Gara, L. D. (2018) · Journal of Experimental Botany · doi:10.1093/jxb/ery168 · Cited by 107
Epigenetic Modifications and Diabetic Retinopathy
Kowluru, R. A., dos Santos, J. M., & Mishra, M. (2013) · BioMed Research International · doi:10.1155/2013/635284 · Cited by 110
The Sperm Epigenome: Implications for the Embryo
Gannon, J. R., Emery, B. R., Jenkins, T. G., & Carrell, D. T. (2013) · Advances in experimental medicine and biology · doi:10.1007/978-1-4614-7783-9_4 · Cited by 105
Mapping epigenetic modifications by sequencing technologies
Chen, X., Xu, H., Shu, X., & Song, C.-X. (2025) · Cell Death & Differentiation · doi:10.1038/s41418-023-01213-1 · Cited by 105
Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains
Brackley, C. A., Liebchen, B., Michieletto, D., Mouvet, F., Cook, P. R., & Marenduzzo, D. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.01.025 · Cited by 98
The genetics of cognitive epigenetics
Kleefstra, T., Schenck, A., Kramer, J. M., & van Bokhoven, H. (2014) · Neuropharmacology · doi:10.1016/j.neuropharm.2013.12.025 · Cited by 114
A review on CRISPR/Cas-based epigenetic regulation in plants
Jogam, P., Sandhya, D., Alok, A., Peddaboina, V., Allini, V. R., & Zhang, B. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.08.182 · Cited by 105
HDAC inhibitors: A new promising drug class in anti-aging research
Pasyukova, E. G., & Vaiserman, A. M. (2017) · Mechanisms of Ageing and Development · doi:10.1016/j.mad.2017.08.008 · Cited by 99
“Among all known histone modifications, acetylation has the highest potential to induce chromatin unfolding, as it neutralizes the electrostatic interaction between the histone and the negatively charged DNA, making it more accessible to the transcriptional apparatus (Zentner and Henikoff, 2013).”
BackgroundChromatin and oxygen sensing in the context of JmjC histone demethylases
Shmakova, A., Batie, M., Druker, J., & Rocha, S. (2014) · Biochemical Journal · doi:10.1042/bj20140754 · Cited by 99
[1,2,4]Triazolo[4,3-a]phthalazines: Inhibitors of Diverse Bromodomains
Fedorov, O., Lingard, H., Wells, C. D., Monteiro, O., Picaud, S., Keates, T., Yapp, C., Philpott, M., Martin, S. J., Felletár, I., et al. (2013) · Journal of Medicinal Chemistry · doi:10.1021/jm401568s · Cited by 99
Epigenetics, chromatin and genome organization: recent advances from the ENCODE project
Siggens, L., & Ekwall, K. (2014) · Journal of Internal Medicine · doi:10.1111/joim.12231 · Cited by 105
Thålin, C., Aguilera, K., Hall, N. W., Marunde, M. R., Burg, J. M., Rosell, A., Daleskog, M., Månsson, M., Hisada, Y., Meiners, M. J., et al. (2020) · Journal of Thrombosis and Haemostasis · doi:10.1111/jth.15003 · Cited by 107
Epigenetic regulation of fetal globin gene expression in adult erythroid cells
Ginder, G. D. (2014) · Translational research · doi:10.1016/j.trsl.2014.05.002 · Cited by 97
“The writers for histone acetylation are histone acetyltransferases including P300/CBP; PCAF and TAF(11)250, (70) as well as histone deacetylases (which might be more properly thought of as “erasers”).”
BackgroundInfluentialMolecular endocrinology of vitamin D on the epigenome level
Carlberg, C. (2017) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2017.03.016 · Cited by 100
“In contrast, other epigenomic marks are very transient, i.e. they last only for a short time (Zentner and Henikoff, 2013).”
BackgroundH3K4me2 functions as a repressive epigenetic mark in plants
Liu, Y., Liu, K., Yin, L., Yu, Y., Qi, J., Shen, W., Zhu, J., Zhang, Y., & Dong, A. (2019) · Epigenetics & Chromatin · doi:10.1186/s13072-019-0285-6 · Cited by 100
Contributions of Histone Variants in Nucleosome Structure and Function
Kurumizaka, H., Kujirai, T., & Takizawa, Y. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.10.012 · Cited by 99
Epigenetic regulation of redox signaling in diabetic retinopathy: Role of Nrf2
Kowluru, R. A., & Mishra, M. (2016) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2016.12.030 · Cited by 99
“Although acetylated form of any lysine moiety of histones results in gene activation, effect of methylation-demethylation, and subsequent gene regulation, depends on the histone, the lysine/ arginine being targeted and the extent of methylation (mono-, di- or trimethylation) [71,74].”
RANKL-responsive epigenetic mechanism reprograms macrophages into bone-resorbing osteoclasts
Bae, S., Kim, K., Kang, K., Kim, H., Lee, M. J., Oh, B., Kaneko, K., Ma, S., Choi, J., Kwak, H., et al. (2022) · Cellular and Molecular Immunology · doi:10.1038/s41423-022-00959-x · Cited by 104
“Histone 3 acetylation at lysine 27 (H3K27ac), an active enhancer mark, is highly enriched in SEs [30].”
BackgroundMatsuda, S., Adachi, J., Ihara, M., Tanuma, N., Shima, H., Kakizuka, A., Ikura, M., Ikura, T., & Matsuda, T. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv967 · Cited by 95
“In the nucleus, histone acetylation drives chromatin structural changes to facilitate DNA transcription, replication and repair (reviewed in (1)).”
BackgroundHDAC1 and HDAC2 in mouse oocytes and preimplantation embryos: Specificity versus compensation
Ma, P., & Schultz, R. M. (2016) · Cell Death and Differentiation · doi:10.1038/cdd.2016.31 · Cited by 95
Plant Epigenetic Stress Memory Induced by Drought: A Physiological and Molecular Perspective
Godwin, J., & Farrona, S. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0179-2_17 · Cited by 94
Mechanisms of Histone Deacetylase Inhibitor-Regulated Gene Expression in Cancer Cells
Chüeh, A. C., Tse, J. W. T., Tögel, L., & Mariadason, J. M. (2014) · Antioxidants and Redox Signaling · doi:10.1089/ars.2014.5863 · Cited by 99
Zhao, W., Xu, Y., Wang, Y., Gao, D., King, J. J., Xu, Y., & Liang, F. (2021) · Scientific Reports · doi:10.1038/s41598-021-95398-5 · Cited by 99
Metadata
- Authors
- Zentner, G. E., & Henikoff, S.
- Affiliations
- Fred Hutch Cancer Center (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Henikoff, Steven
- Venue
- Nature Structural & Molecular Biology
- Published
- 2013-03
- Volume
- 20
- Issue
- 3
- Pages
- 259-266
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- 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
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 ›
Are you an author, or do you see a problem with this page? Request a review