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

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

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

Open this paper in CoChat — free account

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.

Integrity signals

Registry

Crossref · 10.1038/nsmb.2470

Cites

110 of 110 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

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?

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

Show all 111 references

1 of the 111 references couldn’t be matched to a known paper.

Sorted by citations

Items 401–500 of 925

ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements
Perez, A. A., Goronzy, I. N., Blanco, M. R., Yeh, B. T., Guo, J. K., Lopes, C. S., Ettlin, O., Burr, A., & Guttman, M. (2024) · Nature Genetics · doi:10.1038/s41588-024-02000-5 · Cited by 22
“We mapped 15 acetylation marks on all four histone proteins and observed that they colocalize at similar sites genome wide (Pearson r = 0.86–0.97) 81 (Extended Data Fig.”
Influential
Fractal Characterization of Chromatin Decompaction in Live Cells
Yi, J., Stypula‐Cyrus, Y., Blaha, C. S., Roy, H. K., & Backman, V. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.10.014 · Cited by 23
“Chromatin alterations can occur at the nucleosomal level (~10 nm) through modifications of the histones, such as by methylation, acetylation, and phosphorylation (45,46).”
Background
The phytochemical 3,3′-diindolylmethane decreases expression of AR-controlled DNA damage repair genes through repressive chromatin modifications and is associated with DNA damage in prostate cancer cells
Palomera‐Sánchez, Z., Watson, G. W., Wong, C. P., Beaver, L. M., Williams, D. E., Dashwood, R. H., & Ho, E. (2017) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2017.05.005 · Cited by 23
“Many studies have characterized the connection between chromatin modifications such as histone methylation (H3K9me3, H3K27me3, H3K4me3) and transcriptional regulation [19].”
Background
SIN3 LIKE genes mediate long‐day induction of flowering but inhibit the floral transition in short days through histone deacetylation in Arabidopsis
Huang, F., Yuan, W., Tian, S., Zheng, Q., & He, Y. (2019) · The Plant Journal · doi:10.1111/tpj.14430 · Cited by 23
Phospho-ΔNp63α/microRNA network modulates epigenetic regulatory enzymes in squamous cell carcinomas
Ratovitski, E. A. (2014) · Cell Cycle · doi:10.4161/cc.27676 · Cited by 22
“Transcriptional regulation of gene expression, ultimately leading to activation or repression of target genes, involves many layers of control including activating mechanisms, such as demethylation of promoter DNA sequences, acetylation, or demethylation of histones, subsequently affecting chromatin remodeling and rep…”
Background
HDAC superfamily promoters acetylation is differentially regulated by modafinil and methamphetamine in the mouse medial prefrontal cortex
González, B., Bernardi, A., Torres, O. V., Jayanthi, S., Gomez, N. V., Sosa, M. H., García‐Rill, E., Urbano, F. J., Cadet, J. L., & Bisagno, V. (2019) · Addiction Biology · doi:10.1111/adb.12737 · Cited by 22
“Chemical modifications of histones are some of the epigenetic mechanisms that regulate cellular processes requiring DNA access such as transcription, replication, and DNA repair.(1) Among histone modifications, lysine acetylation by histone acetyl‐transferases (HATs) and lysine deacetylation by histone deacetylases (H…”
Background
Combinatorial Histone H3 Modifications Are Dynamically Altered in Distinct Cell Cycle Phases
Lu, C., Coradin, M., Janssen, K. A., Sidoli, S., & Garcia, B. A. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.0c00451 · Cited by 22
“These histone PTMs benchmark DNA readout and play initial roles in epigenetic regulation [8, 9].”
Background
Determinants of epigenetic resistance to HDAC inhibitors in dystrophic fibro‐adipogenic progenitors
Consalvi, S., Tucciarone, L., Macrì, E., Bardi, M. D., Picozza, M., Salvatori, I., Renzini, A., Valente, S., Mai, A., Moresi, V., et al. (2022) · EMBO Reports · doi:10.15252/embr.202254721 · Cited by 26
“…generate different profiles of genome-wide distribution of histone 3 (H3) acetylation at lysines 9/14 (H3K9/14ac) and lysine 27 (H3K27ac) — two major histone modifications associated with a chromatin conformation permissive for gene expression (Zentner & Henikoff, 2013; Tessarz & Kouzarides, 2014).”
High expression levels of microRNA-629, microRNA-525-5p and microRNA-516a-3p in paediatric systemic lupus erythematosus
Zhu, J., Huang, X., Su, G., Wang, L., Wu, F., Zhang, T., & Song, G. (2014) · Clinical Rheumatology · doi:10.1007/s10067-014-2583-5 · Cited by 22
“Recently, some studies have reported on miRNAs that have a close correlation with methylation and histone modification [13, 14].”
Background
Molecular Dynamics Simulations of Bromodomains Reveal Binding‐Site Flexibility and Multiple Binding Modes of the Natural Ligand Acetyl‐Lysine
Spiliotopoulos, D., & Caflisch, A. (2014) · Israel Journal of Chemistry · doi:10.1002/ijch.201400009 · Cited by 22
Monkey-based Research on Human Disease: The Implications of Genetic Differences
Bailey, J. (2014) · Alternatives to Laboratory Animals · doi:10.1177/026119291404200504 · Cited by 22
“This is because they are mechanistically important in the ‘on demand’ de-condensation of chromatin, opening up the structure for the access of enzymes that transcribe, repair and copy the DNA in essential biological processes (86), and are therefore intimately associated with the modulation of gene expression, which,…”
Background
Dynamic modifications of biomacromolecules: mechanism and chemical interventions
Wang, C., Zou, P., Yang, C., Liu, L., Cheng, L., He, X., Zhang, L., Zhang, Y., Jiang, H., & Chen, P. R. (2019) · Science China Life Sciences · doi:10.1007/s11427-019-9823-1 · Cited by 23
Chemical proteomics approaches to examine novel histone posttranslational modifications
Li, X., & Li, X. D. (2014) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2014.10.015 · Cited by 21
Role of epigenetic modulation in cancer stem cell fate
Deshmukh, A. P., Binju, M., Arfuso, F., Newsholme, P., & Dharmarajan, A. (2017) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2017.07.003 · Cited by 21
“Thus, histone modification controls various epigenetic processes and is suspected to be involved in tumor progression (Zentner and Henikoff, 2013).”
Background
Epigenetic Effects in Livestock Breeding
Yakovlev, A. F. (2018) · Russian Journal of Genetics · doi:10.1134/s1022795418080148 · Cited by 22
The effects of biological aging on global DNA methylation, histone modification, and epigenetic modifiers in the mouse germinal vesicle stage oocyte
Marshall, K. L., Wang, J., Ji, T., & Rivera, R. M. (2018) · Animal Reproduction · doi:10.21451/1984-3143-ar2018-0087 · Cited by 21
“Histone acetylation occurs on lysine residues and this post-translational modification is associated with permissive euchromatin and active transcription (Allfrey et al., 1964; Brownell et al., 1996; reviewed in: Zentner and Henikoff, 2013).”
Background
Roles of Histone Acetyltransferases and Deacetylases in the Retinal Development and Diseases
Wang, J., Feng, S., Zhang, Q., Qin, H., Xu, C., Fu, X., Yan, L., Zhao, Y., & Yao, K. (2023) · Molecular Neurobiology · doi:10.1007/s12035-023-03213-1 · Cited by 22
“other DNA-binding proteins, thus affecting DNA transcription, replication, and repair processes [11].”
Background
Epigenetic Regulation in Schizophrenia: Focus on Methylation and Histone Modifications in Human Studies
Delphin, N., Aust, C. E., Griffiths, L. R., & Fernandez, F. (2024) · Genes · doi:10.3390/genes15030272 · Cited by 24
“…do not contribute significantly to the structure of the nucleosomes, but they are essential for regulating chromatin’s degree of condensation into higher-order structures [78] The N-terminal and C-terminal tails of H2A, H2B, H3 and H4 histones are subject to numerous and dynamic modifications.”
Background
Targeting chromatin aging - The epigenetic impact of longevity-associated interventions
Field, A. E., & Adams, P. D. (2016) · Experimental Gerontology · doi:10.1016/j.exger.2016.12.010 · Cited by 22
Post-transcriptional gene silencing, transcriptional gene silencing and human immunodeficiency virus
Méndez, C. (2015) · World Journal of Virology · doi:10.5501/wjv.v4.i3.219 · Cited by 23
Heterochromatin structure: Lessons from the budding yeast
Bi, X. (2014) · IUBMB Life · doi:10.1002/iub.1322 · Cited by 21
“(iii) A nucleosome-binding protein may restrict the dynamics of the nucleosome and “fix” the nucleosome to one of many dynamic positions it can adopt without the protein (25).”
Background
The conformational state of the nucleosome entry–exit site modulates TATA box-specific TBP binding
Hieb, A. R., Gansen, A., Böhm, V., & Langowski, J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku423 · Cited by 20
“One key modification associated with enhanced histone turnover and increased transcriptional activity is the histone acetylation (19) which is also coupled to SAGAdependent remodeling of the nucleosome (64).”
Background
Post-translational modifications of histone and non-histone proteins in epigenetic regulation and translational applications in alcohol-associated liver disease: Challenges and research opportunities
Rungratanawanich, W., Ballway, J. W., Wang, X., Won, K., Hardwick, J. P., & Song, B. (2023) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2023.108547 · Cited by 22
In vitro maturation affects chromosome segregation, spindle morphology and acetylation of lysine 16 on histone H4 in horse oocytes
Franciosi, F., Goudet, G., Tessaro, I. A., Papillier, P., Dalbiès‐Tran, R., Reigner, F., Deleuze, S. C., Douet, C., Miclea, I., Lodde, V., et al. (2015) · Reproduction Fertility and Development · doi:10.1071/rd15350 · Cited by 20
Morphology of nuclear transcription
Weipoltshammer, K., & Schöfer, C. (2016) · Histochemistry and Cell Biology · doi:10.1007/s00418-016-1412-0 · Cited by 20
“The precise topology of active TUs and flanking IGS is still not known in detail.”
BackgroundInfluential
Exploration of the binding pocket of histone deacetylases: the design of potent and isoform-selective inhibitors
Uba, A. İ., & Yelekçi, K. (2017) · TURKISH JOURNAL OF BIOLOGY · doi:10.3906/biy-1701-26 · Cited by 20
Predicting resistance to endocrine therapy in breast cancer: It's time for epigenetic biomarkers (Review)
Fontes‐Sousa, M., Amorim, I., Salta, S., de Sousa, S. P., Henrique, R., & Jerónimo, C. (2019) · Oncology Reports · doi:10.3892/or.2019.6967 · Cited by 20
“Histone methylation, which depending on the residue and the number of methyl groups may lead either to transcription repression or activation (8), is catalyzed by histone methyltransferases (HMTs), while histone demethylation is performed by histone demethylases (HDMs) (7).”
Background
A genetic analysis reveals novel histone residues required for transcriptional reprogramming upon stress
Viéitez, C., Martínez-Cebrián, G., Solé, C., Böttcher, R., Potel, C. M., Savitski, M. M., Onnebo, S. M. N., Fabregat, M., Shilatifard, A., Posas, F., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa081 · Cited by 21
“Histone PTMs play a crucial role in regulating gene expression, thereby facilitating such transcriptional reprogramming (20,32,60,61).”
Background
Epigenetic regulation of temperature responses: past successes and future challenges
Pandey, S. P., Benstein, R. M., Wang, Y., & Schmid, M. (2021) · Journal of Experimental Botany · doi:10.1093/jxb/erab248 · Cited by 20
Erratum: Canonical Wnt signalling regulates nuclear export of Setdb1 during skeletal muscle terminal differentiation
Beyer, S., Pontis, J., Schirwis, E., Battisti, V., Rudolf, A., Grand, F. L., & Ait‐Si‐Ali, S. (2016) · Cell Discovery · doi:10.1038/celldisc.2016.43 · Cited by 21
The roles of inducible chromatin and transcriptional memory in cellular defense system responses to redox-active pollutants
Weinhouse, C. (2021) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2021.03.018 · Cited by 22
Contributions of epigenetic inheritance to the predisposition of major psychiatric disorders: Theoretical framework, evidence, and implications
Varela, R. B., Cararo, J. H., Tye, S. J., Carvalho, A. F., Valvassori, S. S., Fries, G. R., & Quevedo, J. (2022) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2022.104579 · Cited by 21
The TFIIH complex is required to establish and maintain mitotic chromosome structure
Haase, J., Chen, R., Parker, W. M., Bonner, M. K., Jenkins, L. M., & Kelly, A. E. (2021) · bioRxiv · doi:10.7554/elife.75475 · Cited by 16
“…also important for recruiting factors that promote transcription, including the histone acetyltransferase KAT2A which controls histone H3K9 acetylation ( Sandoz et al., 2019 ), a modification that is associated with increased nucleosome turnover ( Aygün et al., 2013 ; Zentner and Henikoff, 2013 ).”
PBRM1 bromodomains associate with RNA to facilitate chromatin association
Silva, S. M. D., Dhiman, A., Sood, S., Mercedes, K. F., Simmons, W. J., Henen, M. A., Vögeli, B., Dykhuizen, E. C., & Musselman, C. A. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad072 · Cited by 19
“The action of the remodelers is tightly regulated by a variety of factors including complex composition and post-translational modification (PTM) of the histone proteins (6), and can also be modulated by association with non-coding RNAs (ncRNA) (7,8).”
Micro- and nanofluidic technologies for epigenetic profiling
Matsuoka, T., Kim, B. C., Moraes, C., Han, M., & Takayama, S. (2013) · Biomicrofluidics · doi:10.1063/1.4816835 · Cited by 19
New insights on chromatin modifiers and histone post‐translational modifications in renal cell tumours
Vieira‐Coimbra, M., Henrique, R., & Jerónimo, C. (2014) · European Journal of Clinical Investigation · doi:10.1111/eci.12360 · Cited by 19
The WOR 1 5′ untranslated region regulates white‐opaque switching in C andida albicans by reducing translational efficiency
Guan, Z., & Liu, H. (2015) · Molecular Microbiology · doi:10.1111/mmi.13014 · Cited by 20
“To investigate this, we transformed a ssd1 deletion mutant (Zentner and Henikoff, 2013) with MAL2p-myc-GFP or MAL2p-UTR-GFP.”
Overlapping Functions between SWR1 Deletion and H3K56 Acetylation in Candida albicans
Guan, Z., & Liu, H. (2015) · Eukaryotic Cell · doi:10.1128/ec.00002-15 · Cited by 20
“Increasing evidence has shown that numerous histone modifications affect nucleosome stability and dynamics by altering the rate of nucleosome turnover and DNA access (2).”
Background
Nucleosomes of polyploid trophoblast giant cells mostly consist of histone variants and form a loose chromatin structure
Hayakawa, K., Terada, K., Takahashi, T., Oana, H., Washizu, M., & Tanaka, S. (2018) · Scientific Reports · doi:10.1038/s41598-018-23832-2 · Cited by 21
Research progress of SIRTs activator resveratrol and its derivatives in autoimmune diseases
Yu, X., Chen, M., Wu, J., & Song, R. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1390907 · Cited by 21
LSD1 knockdown reveals novel histone lysine methylation in human breast cancer MCF-7 cells
Jin, Y., Huo, B., Fu, X., Cheng, Z., Zhu, J., Zhang, Y., Tian, H., & Hu, X. (2017) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2017.05.106 · Cited by 18
The organization of bacterial genomes: Towards understanding the interplay between structure and function
Brocken, D. J. W., Tark‐Dame, M., & Dame, R. T. (2018) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2018.02.007 · Cited by 19
Structural basis for binding diversity of acetyltransferase p300 to the nucleosome
Hatazawa, S., Liu, J., Takizawa, Y., Zandian, M., Negishi, L., Kutateladze, T. G., & Kurumizaka, H. (2022) · iScience · doi:10.1016/j.isci.2022.104563 · Cited by 18
“One of the mechanisms to alleviate the nucleosome-driven suppression involves post-translationalmodifications (PTMs) of histones, particularly acetylations of lysine residues, which change the dynamics and structural properties of the nucleosome (Tessarz and Kouzarides, 2014; Zentner and Henikoff, 2013).”
Background
The Interplay between Dysregulated Metabolism and Epigenetics in Cancer
Bassal, M. A. (2023) · Biomolecules · doi:10.3390/biom13060944 · Cited by 19
A developmental genetic analysis of the lysine demethylase KDM2 mutations in Drosophila melanogaster
Zheng, Y., Hsu, F.-N., Xu, W., Xie, X.-J., Ren, X., Gao, X., Ni, J., & Ji, J. (2014) · Mechanisms of Development · doi:10.1016/j.mod.2014.06.003 · Cited by 18
“Covalent modifications of histone N-terminal tails, such as methylation, acetylation, and phosphorylation, correlate with chromatin structure and seem to influence multiple steps of transcription (Bannister and Kouzarides, 2011; Zentner and Henikoff, 2013).”
Background
Yeats4 drives ILC lineage commitment via activation of Lmo4 transcription
Liu, B., Yang, L., Zhu, X., Li, H., Zhu, P., Wu, J., Lu, T., He, L., Liu, N., Meng, S., et al. (2019) · The Journal of Experimental Medicine · doi:10.1084/jem.20182363 · Cited by 18
“The best-defined histone modifications are composed of acetylation, phosphorylation, methylation, ubiquitination, and sumoylation (Zentner and Henikoff, 2013).”
Molecular Bases of DNA Packaging in Bacteria Revealed by All-Atom Molecular Dynamics Simulations: The Case of Histone-Like Proteins in Borrelia burgdorferi
Hognon, C., Garaudé, S., Timmins, J., Chipot, C. J., Dehez, F., & Monari, A. (2019) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.9b02978 · Cited by 19
Histone epiproteomic profiling distinguishes oligodendroglioma, IDH-mutant and 1p/19q co-deleted from IDH-mutant astrocytoma and reveals less tri-methylation of H3K27 in oligodendrogliomas
Feller, C., Felix, M., Weiss, T., Herold‐Mende, C. C., Zhang, F., Kockmann, T., Sahm, F., Aebersold, R. H., von Deimling, A., & Reuss, D. E. (2019) · Acta Neuropathologica · doi:10.1007/s00401-019-02096-8 · Cited by 18
“Oligodendrogliomas also showed an enrichment of acetylated lysine 9 at histone H2AX (H2AXK9ac) and ubiquitylated lysine 15 on H2AJ (H2AJ K13ac K15ub), two poorly characterised histone modifications that have been linked to DNA damage repair [12, 13].”
Background
Partial Replacement of Nucleosomal DNA with Human FACT Induces Dynamic Exposure and Acetylation of Histone H3 N-Terminal Tails
Tsunaka, Y., Ohtomo, H., Morikawa, K., & Nishimura, Y. (2020) · iScience · doi:10.1016/j.isci.2020.101641 · Cited by 20
Transcriptional memory and response to adverse temperatures in plants
Xie, W., Tang, Q., Yan, F., & Zeng, T. (2021) · Journal of Zhejiang University SCIENCE B · doi:10.1631/jzus.b2100287 · Cited by 20
“Recent studies on the regulatory mechanisms of transcriptional memory of temperature changes have suggested the crucial role of complex epigenetic regu‐ latory networks in these processes (Gong and Miller, 2013; Zentner and Henikoff, 2013; Zhong, 2016).”
Background
Roles of Negatively Charged Histone Lysine Acylations in Regulating Nucleosome Structure and Dynamics
Jing, Y., Li, X., Liu, Z., & Li, X. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.899013 · Cited by 20
Live imaging of H3K9 acetylation in plant cells
Kurita, K., Sakamoto, T., Yagi, N., Sakamoto, Y., Ito, A., Nishino, N., Sako, K., Yoshida, M., Kimurâ, H., Seki, M., et al. (2017) · Scientific Reports · doi:10.1038/srep45894 · Cited by 18
Phenotypes from cell-free DNA
Zukowski, A., Rao, S., & Ramachandran, S. (2020) · Open Biology · doi:10.1098/rsob.200119 · Cited by 18
“PTMs of nucleosomal histones andDNAdiffer in euchromatic regions versus heterochromatic regions [66,67].”
Background
Functional annotation of the animal genomes: An integrated annotation resource for the horse
Peng, S., Dahlgren, A. R., Donnelly, C. G., Hales, E. N., Petersen, J. L., Bellone, R. R., Kalbfleisch, T., & Finno, C. J. (2023) · PLoS Genetics · doi:10.1371/journal.pgen.1010468 · Cited by 17
The diverging epigenomic landscapes of honeybee queens and workers revealed by multiomic sequencing
Zhang, Y., He, X. J., Barron, A. B., Li, Z., Jin, M. J., Wang, Z. L., Huang, Q., Zhang, L. Z., Wu, X. B., Yan, W., et al. (2023) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2023.103929 · Cited by 17
Chromatin epigenomic domain folding: size matters
Caré, B. R., France;, 1. S. U. U. U. P. 0. U. 7. L. F.-7. P., Emeriau, P.-E., Cortini, R., & Victor, J. (2015) · AIMS Biophysics · doi:10.3934/biophy.2015.4.517 · Cited by 17
Control of the gene activity by polycomb and trithorax group proteins in Drosophila
Chetverina, D., Elizar’ev, P. V., Ломаев, Д. В., Georgiev, P. G., & Erokhin, M. (2017) · Russian Journal of Genetics · doi:10.1134/s1022795417020028 · Cited by 17
“Furthermore, acetylation of nucleosomes (H3K27ac), promoted by TrxG proteins, potentially must disrupt the interaction of histones with DNA, neutralizing the positive charge on lysine [213].”
Modulation of transcription factor binding and epigenetic regulation of the MLH1 CpG island and shore by polymorphism rs1800734 in colorectal cancer
Savio, A. J., & Bapat, B. V. (2017) · Epigenetics · doi:10.1080/15592294.2017.1305527 · Cited by 17
“presence or absence of DNA methylation can alter gene expression, histones and their modifications can also alter DNA activity, in part by regulating the degree of accessibility of the DNA to transcription factors or other transcriptional machinery.(15) For example, trimethylation of lysine 27 on histone H3 (H3K27me3)…”
Background
Epigenetic Transitions and Knotted Solitons in Stretched Chromatin
Michieletto, D., Orlandini, E., & Marenduzzo, D. (2017) · Scientific Reports · doi:10.1038/s41598-017-13916-w · Cited by 16
“The set-up involves a reconstituted chromatin fibre [41, 43], which is stretched (e.g., by laser tweezers) and interacts with an ensemble of reader and writer proteins – such as heterochromatin HP1 and SUV39h1 complexes [36, 46] or polycomb [47, 49] enzymes able to bind to and deposit their respective marks.”
Influential
Dynamic changes of histone acetylation and methylation in bovine oocytes, zygotes, and preimplantation embryos
Wu, X., Hu, S., Wang, L., Li, Y., & Yu, H. (2020) · Journal of Experimental Zoology Part B Molecular and Developmental Evolution · doi:10.1002/jez.b.22943 · Cited by 17
Functional analysis of a W heat H omeodomain protein, TaR1 , reveals that host chromatin remodelling influences the dynamics of the switch to necrotrophic growth in the phytopathogenic fungus Z ymoseptoria tritici
Lee, J., Orosa‐Puente, B., Millyard, L., Edwards, M. G., Kanyuka, K., Gatehouse, A. M. R., Rudd, J. J., Hammond-Kosack, K. E., Pain, N., & Sadanandom, A. (2015) · New Phytologist · doi:10.1111/nph.13323 · Cited by 17
Catalysis-dependent stabilization of Bre1 fine-tunes histone H2B ubiquitylation to regulate gene transcriptionPreprint
Wozniak, G. G., & Strahl, B. D. (2014) · Genes & Development · doi:10.1101/gad.243121.114 · Cited by 17
“Histone post-translational modifications (PTMs) play essential roles in the regulation of chromatin structure and function (Kouzarides 2007; Zentner and Henikoff 2013).”
Background
Intracellular localization of histone deacetylase HDA6 in plants
Kurita, K., Sakamoto, Y., Naruse, S., Matsunaga, T., Arata, H. F., Higashiyama, T., Habu, Y., Utsumi, Y., Utsumi, C., Tanaka, M., et al. (2019) · Journal of Plant Research · doi:10.1007/s10265-019-01124-8 · Cited by 16
Photo-Cross-Linking To Delineate Epigenetic Interactome
Zhang, Z., Lin, J., Liu, Z., Tian, G., Li, X., Jing, Y., Li, X., & Li, X. (2022) · Journal of the American Chemical Society · doi:10.1021/jacs.2c06135 · Cited by 17
Genome-Wide Analysis of Snf2 Gene Family Reveals Potential Role in Regulation of Spike Development in Barley
Chen, G., Mishina, K., Zhu, H., Kikuchi, S., Sassa, H., Oono, Y., & Komatsuda, T. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms24010457 · Cited by 16
“The other modulates the specific residues of DNA and histones through adding or removing covalent modifications such as methylation, acetylation, phosphorylation, and ubiquitylation [5].”
Background
Effects of Histone H2B Ubiquitylations and H3K79me3 on Transcription Elongation
Huynh, M., Sengupta, B., Krajewski, W. A., & Lee, T.-H. (2023) · ACS Chemical Biology · doi:10.1021/acschembio.2c00887 · Cited by 16
Diverse modes of regulating methyltransferase activity by histone ubiquitination
Fields, J. K., Hicks, C. W., & Wolberger, C. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102649 · Cited by 16
Role of Epigenetics for the Efficacy of Cisplatin
Lumpp, T., Stößer, S., Fischer, F., Hartwig, A., & Köberle, B. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25021130 · Cited by 18
Rice responds to Spodoptera frugiperda infestation via epigenetic regulation of H3K9ac in the jasmonic acid signaling and phenylpropanoid biosynthesis pathways
Xue, R., Guo, R., Li, Q., Lin, T., Wu, Z., Gao, N., Wu, F., Tong, L., Zeng, R., Song, Y., et al. (2024) · Plant Cell Reports · doi:10.1007/s00299-024-03160-8 · Cited by 16
“…is associated with transcriptional activation, whereas hypoacetylated or methylated histones are sometimes accompanied by transcriptional repression (Shahbazian and Grunstein 2007; Zhou et al. 2010; Li et al. 2011; Liu et al. 2012; Zentner and Henikoff 2013; Song et al. 2020; Xu et al. 2022).”
Roles for Helper T Cell Lineage-Specifying Transcription Factors in Cellular Specialization
Weinmann, A. S. (2014) · Advances in immunology · doi:10.1016/b978-0-12-800147-9.00006-6 · Cited by 16
Epigenética: mecanismos, herança e implicações no melhoramento animal
de Paiva, J. T., de Resende, M. D. V., Resende, R. T., de Oliveira, H. R., Silva, H. T., Caetano, G. C., Lopes, P. S., & Silva, F. F. E. (2019) · Archivos de Zootecnia · doi:10.21071/az.v68i262.4151 · Cited by 16
Role of chromatin, environmental changes and single cell heterogeneity in non-coding transcription and gene regulation
Castelnuovo, M., & Stutz, F. (2015) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2015.04.011 · Cited by 16
Nucleosomes and Epigenetics from a Chemical Perspective
Feng, Y., Endo, M., & Sugiyama, H. (2020) · ChemBioChem · doi:10.1002/cbic.202000332 · Cited by 16
Epigenome, Cancer Prevention and Flavonoids and Curcumin
Stepani, V., Novak, R., & Gall‐Tros̆elj, K. (2014) · InTech eBooks · doi:10.5772/58247 · Cited by 16
New Insights into the Connection Between Histone Deacetylases, Cell Metabolism, and Cancer
Chiaradonna, F., Cirulli, C., Palorini, R., Votta, G., & Alberghina, L. (2014) · Antioxidants and Redox Signaling · doi:10.1089/ars.2014.5854 · Cited by 16
“Histone H1 associates with chromatin outside the core octamer unit and regulates the higher order of the chromatin structure (195).”
Systems approaches to human autoimmune diseases
Banchereau, R., Cepika, A., & Pascual, V. (2013) · Current Opinion in Immunology · doi:10.1016/j.coi.2013.08.005 · Cited by 17
“mRNA expression regulation both pre and post-transcriptionally involves epigenetic mechanisms, including DNA methylation [22], histone modifications [23], non-coding regulatory RNAs such as microRNAs [24] and recently discovered circular non-coding RNAs [25, 26].”
Background
Post-Translational Modification of Human Histone by Wide Tolerance of Acetylation
Li, C., Choi, H.-P., Wang, X., Wu, F., Chen, X., Lü, X., Jing, R., Ryu, H., Wang, X., Azadzoi, K. M., et al. (2017) · Cells · doi:10.3390/cells6040034 · Cited by 16
“Histone acetylation and deacetylation are recognized as major regulatory mechanisms in the activation and repression of gene transcription and regulation of different stages of genetic processes [8].”
Background
Epigenetic Alterations in Hepatocellular Carcinoma: Mechanisms, Biomarkers, and Therapeutic Implications
Wali, A. F., Ansari, A. R., Mir, P. A., El‐Tanani, M., Babiker, R. A., Hussain, M. S., Uppal, J., Zargar, A. I., & Mir, R. H. (2025) · Pharmaceuticals · doi:10.3390/ph18091281 · Cited by 16
“For example, DNA methylation of some miRNA and lncRNA regulators can silence them, but histone changes can affect the availability of their regulating components [141,142].”
A Role for Monomethylation of Histone H3-K27 in Gene Activity inDrosophila
Wang, L., Joshi, P., Miller, E., Higgins, L., Slattery, M. G., & Simon, J. A. (2017) · Genetics · doi:10.1534/genetics.117.300585 · Cited by 15
“…modifications such as methylation,acetylation, phosphorylation, and ubiquitylation are widespread ineukaryotic genomes,where they impactdiverse chromatin processes including transcription, DNA replication and repair, andmitotic progression (Bannister andKouzarides 2011; Zentner and Henikoff 2013).”
Background
Epigenetics in Necrotizing Enterocolitis
Nair, J., & Maheshwari, A. (2021) · Current Pediatric Reviews · doi:10.2174/1573396317666210421110608 · Cited by 15
Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis
Zhang, J., Luo, H., Liu, H., Ye, W., Luo, R., & Chen, H. (2016) · Scientific Reports · doi:10.1038/srep24587 · Cited by 15
Epigenetic regulation of human SOX3 gene expression during early phases of neural differentiation of NT2/D1 cells
Topalović, V., Krstić, A., Schwirtlich, M., Dolfini, D., Mantovani, R., Stevanović, M. J., & Mojsin, M. M. (2017) · PLoS ONE · doi:10.1371/journal.pone.0184099 · Cited by 14
“II [48,49], and observed an increase after the induction of neural differentiation (Fig 5F).”
Background
Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure
Shabane, P. S., & Onufriev, A. V. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.10.017 · Cited by 17
“The structural state of chromatin in-vivo can be modulated in several ways; among the most important are post-translational[8, 9, 1, 10, 11, 12, 13, 14] (PTM) chemical modifications of histone tails, such as acetylation of lysine side-chain, which neutralizes its positive charge.”
Background
Hunting for Darwin's gemmules and Lamarck's fluid: Transgenerational signaling and histone methylation
Choi, Y., & Mango, S. E. (2014) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2014.05.011 · Cited by 15
“One of the models proposed to resolve this issue suggests that local chromatinmodifying enzymes remain associatedwith DNA andmodify newly incorporated histones [40,77].”
Background
Protein N-arginine methyltransferase 5 promotes the tumor progression and radioresistance of nasopharyngeal carcinoma
Yang, D., Liang, T., Gu, Y., Zhao, Y., Shi, Y., Zuo, X., Cao, Q., Yang, Y. P., & Kan, Q. (2015) · Oncology Reports · doi:10.3892/or.2015.4513 · Cited by 15
“Histone modification, a post-translational modification process including methylation, phosphorylation, acetylation, ubiquitination and ADP-ribosylation, can alter the chromatin state or alter the binding affinity of transcription factors to DNA and thus affect gene expression (11,12).”
Background
Histone H4 expression is cooperatively maintained by IKKβ and Akt1 which attenuates cisplatin-induced apoptosis through the DNA-PK/RIP1/IAPs signaling cascade
Wang, R., Zheng, X., Zhang, L., Zhou, B., Hu, H., Li, Z., Zhang, L., Lin, Y., & Wang, X. (2017) · Scientific Reports · doi:10.1038/srep41715 · Cited by 15
Epigenetic interplay at the β-globin locus
Lee, W. S., McColl, B., Maksimovic, J., & Vadolas, J. (2017) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2017.01.014 · Cited by 14
“Histone acetylation – the hallmark of actively transcribed globin genes Acetylation of lysine residues on the tail region of histones is unusual among epigenetic modifications, in that it directly influences the conformation and structure of chromatin [65].”
Background
Chromatin regulators in neurodevelopment and disease: Analysis of fly neural circuits provides insights
Taniguchi, H., & Moore, A. W. (2014) · BioEssays · doi:10.1002/bies.201400087 · Cited by 17
“1) [27], and it is balanced by factors that remove the acetyl groups: histone deacetyltransferases (HDACs) and sirtuins.”
Background
Muscle-relevant genes marked by stable H3K4me2/3 profiles and enriched MyoD binding during myogenic differentiation
Cui, H., Bansal, V., Grunert, M., Malecová, B., Dall’Agnese, A., Latella, L., Gatto, S., Ryan, T. L., Schulz, K., Chen, W., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0179464 · Cited by 15
Simulations suggest pharmacological methods for rescuing long-term potentiation
Smolen, P., Baxter, D. A., & Byrne, J. H. (2014) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2014.07.006 · Cited by 13
“Multiple acetylations are believed to induce an “open” chromatin conformation allowing gene induction (Zentner and Henikoff, 2013).”
Background
Induction of senescence upon loss of the Ash2l core subunit of H3K4 methyltransferase complexes
Bochyńska, A., Stenzel, A. T., Sayadi-Boroujeni, R., Kuo, C., Barsoum, M., Liang, W., Bussmann, P., Costa, I. G., Lüscher‐Firzlaff, J., & Lüscher, B. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac591 · Cited by 14
Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes reduces chromatin accessibility at promoters
Barsoum, M., Stenzel, A. T., Bochyńska, A., Kuo, C., Tsompanidis, A., Sayadi-Boroujeni, R., Bussmann, P., Lüscher‐Firzlaff, J., Costa, I. G., & Lüscher, B. (2022) · Scientific Reports · doi:10.1038/s41598-022-25881-0 · Cited by 15
The patterns and participants of parental histone recycling during DNA replication in Saccharomyces cerevisiae
Shan, Z., Zhang, Y., Bu, J., Li, H., Zhang, Z., Xiong, J., & Zhu, B. (2023) · Science China Life Sciences · doi:10.1007/s11427-022-2267-6 · Cited by 13
“Active chromatin is characterized by higher accessibility and faster histone turnover than heterochromatin (Zentner and Henikoff, 2013).”
Background
Neurotoxic effects induced by flunitrazepam and its metabolites in zebrafish: Oxidative stress, apoptosis, and histone hypoacetylation
Qin, Y., Huang, Y., Lin, W., Huang, R., Li, K., Han, X., & Ren, Y. (2024) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2024.170521 · Cited by 14
HBO1, a MYSTerious KAT and its links to cancer
Yokoyama, A., Niida, H., Kutateladze, T. G., & Côté, J. (2024) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2024.195045 · Cited by 14
Histone Demethylases in Cancer
Sainathan, S. K., Paul, S., Ramalingam, S., Baranda, J. C., Anant, S., & Dhar, A. (2015) · Current Pharmacology Reports · doi:10.1007/s40495-015-0025-y · Cited by 14
Cell-Free Circulating Epimarks in Cancer Monitoring
Duforestel, M., Briand, J., Bougras-Cartron, G., Heymann, D., Frenel, J., Vallette, F. M., & Cartron, P. (2020) · Epigenomics · doi:10.2217/epi-2019-0170 · Cited by 15
Tlx3 Promotes Glutamatergic Neuronal Subtype Specification through Direct Interactions with the Chromatin Modifier CBP
Shimomura, A., Patel, D., Wilson, S. M., Koehler, K. R., Khanna, R., & Hashino, E. (2015) · PLoS ONE · doi:10.1371/journal.pone.0135060 · Cited by 14
Early free access to hypertonic NaCl solution induces a long-term effect on drinking, brain cell activity and gene expression of adult rat offspring
Macchione, A. F., Beas, C., Dadam, F., Caeiro, X. E., Godino, A., Ponce, L. F., Amigone, J. L., & Vivas, L. (2015) · Neuroscience · doi:10.1016/j.neuroscience.2015.04.004 · Cited by 13
Understanding the chromatin remodeling code
Ha, M. (2013) · Plant Science · doi:10.1016/j.plantsci.2013.07.006 · Cited by 15

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

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

Regulation of nucleosome dynamics by histone modifications

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks