Cited by 2,267Epigenetics and DNA MethylationGenomics and Chromatin DynamicsCancer-related gene regulation

The DOI matches its Crossref record; 108 of the 108 references it cites were found in a registry or an index.

Linking DNA methylation and histone modification: patterns and paradigms

Cedar, Howard, Bergman, Yehudit·2009·Nature Reviews Genetics

Open this paper in CoChat — free account

Abstract

Both DNA methylation and histone modification are involved in establishing patterns of gene repression during development. Certain forms of histone methylation cause local formation of heterochromatin, which is readily reversible, whereas DNA methylation leads to stable long-term repression. It has recently become apparent that DNA methylation and histone modification pathways can be dependent on one another, and that this crosstalk can be mediated by biochemical interactions between SET domain histone methyltransferases and DNA methyltransferases. Relationships between DNA methylation and histone modification have implications for understanding normal development as well as somatic cell reprogramming and tumorigenesis.

Integrity signals

Registry

Crossref · 10.1038/nrg2540

Cites

108 of 108 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?

Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors
Takahashi, K., & Yamanaka, S. (2006) · Cell · doi:10.1016/j.cell.2006.07.024 · Cited by 26,673
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845
DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development
Okano, M., Bell, D. W., Haber, D. A., & Li, E. (1999) · Cell · doi:10.1016/s0092-8674(00)81656-6 · Cited by 6,143
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.041 · Cited by 5,361
The Epigenomics of Cancer
Jones, P. A., & Baylin, S. B. (2007) · Cell · doi:10.1016/j.cell.2007.01.029 · Cited by 4,515
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
Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex
Nan, X., Ng, H.-H., Johnson, C. A., Laherty, C. D., Turner, B. M., Eisenman, R. N., & Bird, A. (1998) · Nature · doi:10.1038/30764 · Cited by 3,440
DNA methylation landscapes: Provocative insights from epigenomics
Suzuki, M. M., & Bird, A. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2341 · Cited by 3,039
Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription
Jones, P. L., Veenstra, G. J. C., Wade, P. A., Vermaak, D., Kass, S. U., Landsberger, N., Strouboulis, J., & Wolffe, A. P. (1998) · Nature Genetics · doi:10.1038/561 · Cited by 2,791
In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state
Wernig, M., Meissner, A., Foreman, R. K., Brambrink, T., Ku, M., Hochedlinger, K., Bernstein, B., & Jaenisch, R. (2007) · Nature · doi:10.1038/nature05944 · Cited by 2,732

Flagged first, then by citations

Show all 108 references

Sorted by citations

Items 401–500 of 1,003

Diabetic retinopathy, metabolic memory and epigenetic modifications
Kowluru, R. A. (2017) · Vision Research · doi:10.1016/j.visres.2017.02.011 · Cited by 88
Overcoming Immune Checkpoint Blockade Resistance via EZH2 Inhibition
Kim, H. J., Cantor, H., & Cosmopoulos, K. (2020) · Trends in Immunology · doi:10.1016/j.it.2020.08.010 · Cited by 88
Epigenetic Mechanisms of Genomic Imprinting: Common Themes in the Regulation of Imprinted Regions in Mammals, Plants, and Insects
MacDonald, W. A. (2012) · Genetics Research International · doi:10.1155/2012/585024 · Cited by 89
“Histone modifications and DNA methylation are often intertwined, each epigenetic mark can influence the other’s recruitment to reinforce differential epigenetic states [25, 26].”
Background
Extensive histone post-translational modification in honey bees
Dickman, M. J., Kucharski, R., Maleszka, R., & Hurd, P. J. (2012) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2012.11.003 · Cited by 87
Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences
Tao, Y., Xi, S., Shan, J., Maunakea, A. K., Che, A., Briones, V. R., Lee, E. Y., Geiman, T. M., Huang, J., Stephens, R. M., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1017000108 · Cited by 89
Differential Volatile Signatures from Skin, Naevi and Melanoma: A Novel Approach to Detect a Pathological Process
Abaffy, T., DUNCAN, R. C., Riemer, D. D., Tietje, O., Elgart, G. W., Milikowski, C., & DeFazio, R. A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013813 · Cited by 89
“It has been shown that cancer cells are subject to abnormal de novo methylation [39].”
Recruitment and Biological Consequences of Histone Modification of H3K27me3 and H3K9me3
Kim, J. H., & Kim, H. (2012) · ILAR Journal · doi:10.1093/ilar.53.3-4.232 · Cited by 94
“Several studies involving biochemical purifi cations indeed confi rmed that isolated multiprotein complexes usually contain both histone and DNA methylases (Cedar and Bergman 2009).”
Background
Cyst Nematode Parasitism Induces Dynamic Changes in the Root Epigenome
Hewezi, T., Lane, T. S., Piya, S., Rambani, A., Rice, J. H., & Staton, M. E. (2017) · PLANT PHYSIOLOGY · doi:10.1104/pp.16.01948 · Cited by 90
“Because of the mutual associations between histone modifications and DNA methylation during initiation and maintenance of repressed states of genes (Cedar and Bergman, 2009; To et al., 2011; Liu et al., 2012), it is conceivable that demethylation at specific promoter regions may require active…”
Background
Genetic alterations in adult T‐cell leukemia/lymphoma
Kogure, Y., & Kataoka, K. (2017) · Cancer Science · doi:10.1111/cas.13303 · Cited by 91
The Role of Host Cell DNA Methylation in the Immune Response to Bacterial Infection
Qin, W., Scicluna, B. P., & van der Poll, T. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.696280 · Cited by 91
Epigenetic modulation of Fgf21 in the perinatal mouse liver ameliorates diet-induced obesity in adulthood
Yuan, X.-M., Tsujimoto, K., Hashimoto, K., Kawahori, K., Hanzawa, N., Hamaguchi, M., Seki, T., Nawa, M., Ehara, T., Kitamura, Y., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03038-w · Cited by 77
Linking cell signaling and the epigenetic machinery
Mohammad, H. P., & Baylin, S. B. (2010) · Nature Biotechnology · doi:10.1038/nbt1010-1033 · Cited by 85
Epigenetic silencing of chemokine CCL2 represses macrophage infiltration to potentiate tumor development in small cell lung cancer
Zheng, Y., Wang, Z., Wei, S., Liu, Z., & Chen, G. (2020) · Cancer Letters · doi:10.1016/j.canlet.2020.11.034 · Cited by 84
Induction of p16INK4a Is the Major Barrier to Proliferation when Epstein-Barr Virus (EBV) Transforms Primary B Cells into Lymphoblastoid Cell Lines
Skalska, L., White, R. E., Parker, G. A., Sinclair, A. J., Paschos, K., & Allday, M. J. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003187 · Cited by 87
“It is well established that polycomb-mediated gene repression is often a precursor to promoter DNA methylation (reviewed in [7,56]), so it is reasonable to hypothesize that the B cells reprogrammed in vivo by EBV will be particularly prone to aberrant DNA methylation at the CDKN2A and BCL2L11 loci during tumorigenesis.”
Background
Epigenetic Switching by the Metabolism-sensing Factors in the Generation of Orexin Neurons from Mouse Embryonic Stem Cells
Hayakawa, K., Hirosawa, M., Tabei, Y., Arai, D., Tanaka, S., Murakami, N., Yagi, S., & Shiota, K. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.455899 · Cited by 86
Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states
Haerter, J. O., Lövkvist, C., Dodd, I. B., & Sneppen, K. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1235 · Cited by 82
“Although we have not modeled it explicitly, collaboration could also work in more indirect ways, for example, by reciprocal feedback between specific nucleosome modifications and DNA methylation enzymes (1,42), as proposed for maintainance of CHG methylation in plants by recruitment of the CMT3 DNA methylase by the H3…”
Background
Digging deep into “dirty” drugs – modulation of the methylation machinery
Pleyer, L., & Greil, R. (2015) · Drug Metabolism Reviews · doi:10.3109/03602532.2014.995379 · Cited by 84
“…of crosstalk between DNA methylation and histone post-translational modifications, whereby histone modifications are thought to provide labile transcriptional repression, and DNA methylation results in more permanent gene silencing (Cedar & Bergman, 2009; Ikegami et al., 2009; Raynal et al., 2012).”
Background
Understanding Epigenetics in the Neurodegeneration of Alzheimer’s Disease: SAMP8 Mouse Model
Griñán‐Ferré, C., Corpas, R., Puigoriol‐Illamola, D., Palomera‐Ávalos, V., Sanfeliu, C., & Pallàs, M. (2018) · Journal of Alzheimer s Disease · doi:10.3233/jad-170664 · Cited by 86
“include Histone DeACetylases family (HDACs) [36].”
Potential Effects of Environmental Chemical Contamination in Congenital Heart Disease
Gorini, F., Chiappa, E., Gargani, L., & Picano, E. (2014) · Pediatric Cardiology · doi:10.1007/s00246-014-0870-1 · Cited by 90
A novel miR-193a-5p-YY1-APC regulatory axis in human endometrioid endometrial adenocarcinoma
Yang, Y., Zhou, L., Lu, L., Wang, L., Li, X., Jiang, P., Chan, L. K. Y., Zhang, T., Yu, J. Q., Kwong, J., et al. (2012) · Oncogene · doi:10.1038/onc.2012.360 · Cited by 84
Genomic Imprinting in the Arabidopsis Embryo Is Partly Regulated by PRC2
Raissig, M. T., Bemer, M., Baroux, C., & Grossniklaus, U. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003862 · Cited by 84
“Especially histone modifications might be of importance since they are more readily reversible than DNA methylation [55] and different modifications have been associated with imprinted genes in maize [56].”
Background
Totipotency and lineage segregation in the human embryo
Paepe, C. D., Krivega, M., Cauffman, G., Geens, M., & de Velde, H. V. (2014) · Molecular Human Reproduction · doi:10.1093/molehr/gau027 · Cited by 84
Alternation of histone and DNA methylation in human atherosclerotic carotid plaques
Napieralski, R., Wagner, E., Gebhard, H., Schmitt, M., Zimmermann, A., Eckstein, H.-H., Greißel, A., Culmes, M., Zernecke, A., & Pelisek, J. (2015) · Thrombosis and Haemostasis · doi:10.1160/th14-10-0852 · Cited by 83
“Recent evidence indicates that both modifications may be accomplished through direct interactions between histone and DNA methyltransferases (6).”
Background
Epigenetic dynamics in psychiatric disorders: Environmental programming of neurodevelopmental processes
Kofink, D., Boks, M. P. M., Timmers, H. T. M., & Kas, M. J. (2013) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2013.03.020 · Cited by 83
Molecular Nutrition Research—The Modern Way Of Performing Nutritional Science
Norheim, F., Gjelstad, I., Hjorth, M., Vinknes, K., Langleite, T., Holen, T., Jensen, J., Dalen, K., Karlsen, A., Kielland, A., et al. (2012) · Nutrients · doi:10.3390/nu4121898 · Cited by 83
“DNA methylation is one of the major epigenetic modulators [64]; it can suppress gene expression by modulating the access of the transcript machinery to the chromatin or by recruiting methyl-binding proteins [65].”
Background
The Gut Microbiota and their Metabolites: Potential Implications for the Host Epigenome
Mischke, M., & Plösch, T. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-31248-4_3 · Cited by 86
The effects of Arabidopsis genome duplication on the chromatin organization and transcriptional regulation
Zhang, H., Zheng, R., Wang, Y.-L., Zhang, Y., Hong, P., Fang, Y.-P., Li, G., & Fang, Y.-D. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz511 · Cited by 64
“It was known that H3K4me3 is an active marker while H3K27me3 a repressive marker of gene expression (67).”
Background
Epigenetics of Sepsis
Binnie, A., Tsang, J. L. Y., Hu, P., Carrasqueiro, G., Castelo‐Branco, P., & dos Santos, C. C. (2020) · Critical Care Medicine · doi:10.1097/ccm.0000000000004247 · Cited by 84
“Other marks, such as methylation of histone H3 at lysine 27 (H3K27me), are associated with gene repression (30).”
Background
De Novo DNA Methylation Is Required to Restrict T Helper Lineage Plasticity
Thomas, R. M., Gamper, C. J., Ladle, B. H., Powell, J. D., & Wells, A. D. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.312785 · Cited by 83
A Relay Race on the Evolutionary Adaptation Spectrum
Yona, A. H., Frumkin, I., & Pilpel, Y. (2015) · Cell · doi:10.1016/j.cell.2015.10.005 · Cited by 80
High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions
Krebs, A. R., Dessus-Babus, S., Burger, L., & Schübeler, D. (2014) · eLife · doi:10.7554/elife.04094 · Cited by 81
“From sequence perspective, these include binding of unmethylated CGs by CXXC domain containing proteins, which have been proposed to inhibit or counteract methyltransferase activity directly or through the establishment of a specific chromatin state (Ooi et al., 2007; Cedar and Bergman, 2009).”
Background
Epigenetic performers in plants‡
Chen, M., Lv, S., & Meng, Y. (2010) · Development Growth & Differentiation · doi:10.1111/j.1440-169x.2010.01192.x · Cited by 84
“The review completed by Cedar & Bergman (2009) on the correlations between DNA methylation and histone modification in mammals provided significant examples that could be applied to plant research.”
Background
Targeting histone methyltransferase EZH2 as cancer treatment
Kondo, Y. (2014) · The Journal of Biochemistry · doi:10.1093/jb/mvu054 · Cited by 82
The ambiguous nature of epigenetic responsibility
Dupras, C., & Ravitsky, V. (2016) · Journal of Medical Ethics · doi:10.1136/medethics-2015-103295 · Cited by 81
Blood volatile compounds as biomarkers for colorectal cancer
Wang, C., Li, P., Lian, A., Sun, B., Wang, X., Guo, L., Chi, C., Liu, S., Zhao, W., Luo, S., et al. (2013) · Cancer Biology & Therapy · doi:10.4161/cbt.26723 · Cited by 82
The histone variant H2A.X is a regulator of the epithelial–mesenchymal transition
Weyemi, U., Redon, C. E., Choudhuri, R., Aziz, T., Maeda, D., Boufraqech, M., Parekh, P. R., Sethi, T. K., Kasoji, M., Abrams, N., et al. (2016) · Nature Communications · doi:10.1038/ncomms10711 · Cited by 80
Phenobarbital Mediates an Epigenetic Switch at the Constitutive Androstane Receptor (CAR) Target Gene Cyp2b10 in the Liver of B6C3F1 Mice
Lempiäinen, H., Müller, A., Brasa, S., Teo, S.-S., Roloff, T. C., Morawiec, L., Zamurovic, N., Vicart, A., Funhoff, E. G., Couttet, P., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018216 · Cited by 81
“The coordinated interplay of different layers of epigenetic regulation (such as DNA methylation and post-translational modifications (PTMs) of histone proteins) provide a dynamic platform for functionally organizing the genome in a developmental-stage and cell-type specific manner [1,2,3,4,5,6,7,8,9].”
Background
Aging and peripheral lipopolysaccharide can modulate epigenetic regulators and decrease IL-1β promoter DNA methylation in microglia
Matt, S. M., Lawson, M. A., & Johnson, R. W. (2016) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2016.07.006 · Cited by 84
“Histone modifications also have a close relationship with DNA methylation, and could be more influential on DNA methylation and transcription of some genes compared to others (Cedar and Bergman, 2009).”
Background
RETRACTED ARTICLE: Lnc-PDZD7 contributes to stemness properties and chemosensitivity in hepatocellular carcinoma through EZH2-mediated ATOH8 transcriptional repression
Zhang, Y., Tang, B., Song, J. H., Yu, S., Yang, L., Su, H., & He, S. (2019) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-019-1106-2 · Cited by 81
Retracted
Multiple Levels of PGC-1α Dysregulation in Heart Failure
Oka, S., Sabry, A. D., Cawley, K. M., & Warren, J. S. (2020) · Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2020.00002 · Cited by 85
Copper: An Intracellular Achilles’ Heel Allowing the Targeting of Epigenetics, Kinase Pathways, and Cell Metabolism in Cancer Therapeutics
Michniewicz, F., Saletta, F., Rouaen, J. R. C., Hewavisenti, R., Mercatelli, D., Cirillo, G., Giorgi, F. M., Trahair, T. N., Ziegler, D. S., & Vittorio, O. (2021) · ChemMedChem · doi:10.1002/cmdc.202100172 · Cited by 81
Epigenetics and the overhealing wound: the role of DNA methylation in fibrosis
Neary, R., Watson, C. J., & Baugh, J. A. (2015) · Fibrogenesis & Tissue Repair · doi:10.1186/s13069-015-0035-8 · Cited by 83
“which are capable of recruiting histone deacetylases to the methylated region [25].”
Background
Genetic and epigenetic control of gene expression by CRISPR–Cas systems
Lo, A., & Qi, L. (2017) · F1000Research · doi:10.12688/f1000research.11113.1 · Cited by 72
Epigenetic regulation of hypoxia‐responsive gene expression: Focusing on chromatin and DNA modifications
Tsai, Y., & Wu, K. (2013) · International Journal of Cancer · doi:10.1002/ijc.28190 · Cited by 83
Maternal high-zinc diet attenuates intestinal inflammation by reducing DNA methylation and elevating H3K9 acetylation in the A20 promoter of offspring chicks
Li, C., Guo, S., Gao, J., Guo, Y., Du, E., Lv, Z., & Zhang, B. (2014) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2014.10.005 · Cited by 80
Global profiling of histone and DNA methylation reveals epigenetic-based regulation of gene expression during epithelial to mesenchymal transition in prostate cells
Ke, X., Qu, Y., Yang, C. Z., Li, W., Rotter, V., Oyan, A. M., & Kalland, K. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-669 · Cited by 82
“All these findings were different from the prevailing view that DNAMe plays the critical role in silencing gene expression [6,23].”
BackgroundInfluential
Exercise training alters the genomic response to acute exercise in human adipose tissue
Fabre, O., Ingerslev, L., Garde, C., Donkin, I., Simar, D., & Barrès, R. (2018) · Epigenomics · doi:10.2217/epi-2018-0039 · Cited by 71
Human Endometrial DNA Methylome Is Cycle-Dependent and Is Associated With Gene Expression Regulation
Houshdaran, S., Zelenko, Z., Irwin, J. C., & Giudice, L. C. (2014) · Molecular Endocrinology · doi:10.1210/me.2013-1340 · Cited by 81
Epigenetic regulation of neurogenesis in the adult hippocampus
Covic, M., Karaca, E., & Lie, D. C. (2010) · Heredity · doi:10.1038/hdy.2010.27 · Cited by 83
“…catalyze trimethylation of lysine 27 of histone 3 (H3K27me3), which leads to transcriptional repression through local heterochromatin formation (for review, see Cedar and Bergman (2009)) and/or inhibition of transcriptional elongation through stalling of RNA polymerase II (Stock et al., 2007).”
Background
Molecular and Enzymatic Profiles of Mammalian DNA Methyltransferases: Structures and Targets for Drugs
Xu, F., Mao, C., Ding, Y., Rui, C., Wu, L., Shi, A., Zhang, H., Zhang, L., & Xu, Z. (2010) · Current Medicinal Chemistry · doi:10.2174/092986710793205372 · Cited by 80
Hypermethylation at loci sensitive to the prenatal environment is associated with increased incidence of myocardial infarction
Talens, R. P., Jukema, J. W., Trompet, S., Kremer, D., Westendorp, R. G. J., Lumey, L. H., Sattar, N. A., Putter, H., Slagboom, P. E., & Heijmans, B. T. (2011) · International Journal of Epidemiology · doi:10.1093/ije/dyr153 · Cited by 80
Epigenetic Regulation of Cytochrome P450 Enzymes and Clinical Implication
Tang, X., & Chen, S. (2015) · Current Drug Metabolism · doi:10.2174/138920021602150713114159 · Cited by 82
Evidence for the implication of the histone code in building the genome structure
Prakash, K., & Fournier, D. (2017) · Biosystems · doi:10.1016/j.biosystems.2017.11.005 · Cited by 82
Enhancer-Driven lncRNA BDNF-AS Induces Endocrine Resistance and Malignant Progression of Breast Cancer through the RNH1/TRIM21/mTOR Cascade
Lin, X., Dinglin, X.-X., Cao, S., Zheng, S., Wu, C., Chen, W., Li, Q., Hu, Q., Zheng, F., Wu, Z., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107753 · Cited by 78
Alteration of gut microbiota affects expression of adiponectin and resistin through modifying DNA methylation in high-fat diet-induced obese mice
Yao, H., Fan, C., Lu, Y., Fan, X., Xia, L., Li, P., Wang, R., Tang, T., Wang, Y., & Qi, K. (2020) · Genes & Nutrition · doi:10.1186/s12263-020-00671-3 · Cited by 79
Epigenetics and pulmonary diseases in the horizon of precision medicine: a review
Benincasa, G., DeMeo, D. L., Glass, K., Silverman, E. K., & Claudio Napoli, A. (2020) · European Respiratory Journal · doi:10.1183/13993003.03406-2020 · Cited by 85
Epigenetic mechanisms regulate NADPH oxidase-4 expression in cellular senescence
Sanders, Y. Y., Liu, H., Liu, G., & Thannickal, V. J. (2014) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2014.12.008 · Cited by 78
NF-κB Induction of the SUMO Protease SENP2: A Negative Feedback Loop to Attenuate Cell Survival Response to Genotoxic Stress
Lee, M. H., Mabb, A. M., Gill, G., Yeh, E. T. H., & Miyamoto, S. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.06.017 · Cited by 84
“During initiation of transcription, methylation of histone H3 lysine 4 (H3K4) increases the access of the transcription machinery (Cedar and Bergman, 2009; Natoli, 2010).”
EZH2 Promotes Malignant Behaviors via Cell Cycle Dysregulation and Its mRNA Level Associates with Prognosis of Patient with Non-Small Cell Lung Cancer
Cao, W., Ribeiro, R. D. O., Liu, D., Saintigny, P., Xia, R., Xue, Y., Lin, R., Mao, L., & Ren, H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0052984 · Cited by 80
“H3K27Me3 will in turn serve as a landmark for recruitment of other protein complexes, such as PRC1, to mediate epigenetic silencing [13].”
Background
Reprogramming during epithelial to mesenchymal transition under the control of TGFβ
Tan, E., Olsson, A.-K., & Moustakas, A. (2014) · Cell Adhesion & Migration · doi:10.4161/19336918.2014.983794 · Cited by 78
“Long-term silencing of genes is achieved through DNA methylation, in which DNMTs methylate the C5 position of cytosine in CpG dinucleotides.(97) De novo DNA methylation of several promoters, most notably of the E-cadherin gene, occurs in human mammary epithelial and breast cancer cells undergoing EMT.”
Background
Theory Uncovers an Unusual Mechanism of DNA Repair of a Lesioned Adenine by AlkB Enzymes
Wang, B., Usharani, D., Li, C., & Shaik, S. S. (2014) · Journal of the American Chemical Society · doi:10.1021/ja507934g · Cited by 79
Epigenetic role of thymoquinone: impact on cellular mechanism and cancer therapeutics
Khan, M. A., Tania, M., & Fu, J. (2019) · Drug Discovery Today · doi:10.1016/j.drudis.2019.09.007 · Cited by 82
Epigenetic modification and therapeutic targets of diabetes mellitus
Singh, R., Chandel, S., Dey, D., Ghosh, A., Roy, S., Ravichandiran, V., & Ghosh, D. (2020) · Bioscience Reports · doi:10.1042/bsr20202160 · Cited by 85
One-carbon metabolism and epigenetic regulation of embryo development
Xu, J., & Sinclair, K. D. (2015) · Reproduction Fertility and Development · doi:10.1071/rd14377 · Cited by 81
“In addition, modifications to DNA and histone methylation are carefully orchestrated to modulate gene expression programming in the organism through direct interactions between histone and DNMTs (Cedar and Bergman 2009).”
Background
True Lies: The Double Life of the Nucleotide Excision Repair Factors in Transcription and DNA Repair
May, N. L., Egly, J., & Coin, F. (2010) · Journal of Nucleic Acids · doi:10.4061/2010/616342 · Cited by 78
“Active DNA demethylation at promoters is intimately linked with histones posttranslational modifications (PTMs) [49].”
Metabolic regulation of stem cell function
Burgess, R., Agathocleous, M., & Morrison, S. J. (2014) · Journal of Internal Medicine · doi:10.1111/joim.12247 · Cited by 81
Sirtuins and Cancer: Role in the Epithelial‐Mesenchymal Transition
Palmirotta, R., Cives, M., Della‐Morte, D., Capuani, B., Lauro, D., Guadagni, F., & Silvestris, F. (2016) · Oxidative Medicine and Cellular Longevity · doi:10.1155/2016/3031459 · Cited by 77
“phenotype largely relies on different rounds of histone acetylation and DNA methylation, driving the interconversion of facultative heterochromatin into an active euchromatic state and vice versa [49, 52].”
Background
Distinct Enhancer Activity of Oct4 in Naive and Primed Mouse Pluripotency
Choi, H. W., Joo, J. Y., Hong, Y. J., Kim, J. S., Song, H., Lee, J.-W., Wu, G., Schöler, H. R., & Do, J. T. (2016) · Stem Cell Reports · doi:10.1016/j.stemcr.2016.09.012 · Cited by 78
“Since both DNA methylation and histone modification regulate gene expression and affect each other (Cedar and Bergman, 2009), we next examined the DNA methylation pattern of the Oct4 regulatory elements.”
Background
A Primer on Concepts and Applications of Proteomics in Neuroscience
Hosp, F., & Mann, M. (2017) · Neuron · doi:10.1016/j.neuron.2017.09.025 · Cited by 80
Can epigenetics translate environmental cues into phenotypes?
Norouzitallab, P., Baruah, K., Vanrompay, D. C. G., & Bossier, P. (2018) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2018.08.063 · Cited by 84
Metal carcinogen exposure induces cancer stem cell-like property through epigenetic reprograming: A novel mechanism of metal carcinogenesis
Wang, Z., & Yang, C. (2019) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2019.01.002 · Cited by 79
“For example, certain tumor suppressor gene promoter CpG island hypermethylation is usually associated with gain of repressive H3K9 methylation and H3K27 trimethylation [34-36].”
Background
The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiationPreprint
Zhao, L., Sun, M.-A., Li, Z., Bai, X., Yu, M., Wang, M., Liang, L., Shao, X., Arnovitz, S., Wang, Q., et al. (2014) · Genome Research · doi:10.1101/gr.163147.113 · Cited by 78
“Directed by RNApolymerase II, histoneH3 andH4 acetylation and H3K4 methylation on CGIs prevent DNMT3L from accessing the chromatin and inhibit de novo DNAmethylation (Guenther et al. 2007; Ooi et al. 2007; Cedar and Bergman 2009).”
Background
DNA Methylation and Its Implications and Accessibility for Neuropsychiatric Therapeutics
Day, J. J., Kennedy, A. J., & Sweatt, J. D. (2015) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010814-124527 · Cited by 78
“A large variety of epigenetic modifications can occur on histones, including phosphorylation, acetylation, and alkylation, many of which have profound effects on DNA availability and the recruitment of transcriptional elements (1).”
Background
Tissue-specific demethylation in CpG-poor promoters during cellular differentiation
Nagae, G., Isagawa, T., Shiraki, N., Fujita, T., Yamamoto, S., Tsutsumi, S., Nonaka, A., Yoshiba, S., Matsusaka, K., Midorikawa, Y., et al. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr170 · Cited by 76
“To date, the exploration of tDMRs was performed on the premise that stepwise addition of promoter methylation contributes to cell fate determination during early embryogenesis (26,27).”
Background
Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes
Stern, J. L., Paucek, R. D., Huang, F. W., Ghandi, M., Nwumeh, R., Costello, J. C., & Cech, T. R. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.12.001 · Cited by 77
ZNF711 down-regulation promotes CISPLATIN resistance in epithelial ovarian cancer via interacting with JHDM2A and suppressing SLC31A1 expression
Wu, G., Peng, H., Tang, M., Yang, M., Wang, J., Hu, Y., Li, Z., Li, Z., Li, Z., & Song, L. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103558 · Cited by 77
Arabidopsis VIM Proteins Regulate Epigenetic Silencing by Modulating DNA Methylation and Histone Modification in Cooperation with MET1
Kim, J., Kim, J. H., Richards, E. J., Chung, K. M., & Woo, H. R. (2014) · Molecular Plant · doi:10.1093/mp/ssu079 · Cited by 77
DNA methylation in obesity and type 2 diabetes
de Mello, V. D., Pulkkinen, L., Lalli, M., Kolehmainen, M., Pihlajamäki, J., & Uusitupa, M. I. J. (2014) · Annals of Medicine · doi:10.3109/07853890.2013.857259 · Cited by 78
Endocrine disrupters: the new players able to affect the epigenome
Casati, L., Sendra, R., Sibilia, V., & Celotti, F. (2015) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2015.00037 · Cited by 76
“Among them, the modifications more extended are acetylation, methylation, phosphorylation, ubiquitination, sumoylation, and ADP ribosylation (Cedar and Bergman, 2009).”
Background
Locking the genome: nuclear organization and cell fate
Meister, P., Mango, S. E., & Gasser, S. M. (2011) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2011.01.023 · Cited by 82
“com both repressive and active histone tail modifications, DNA methylation and the accessibility of transcription factor binding sites to their ligands [2–6].”
Background
Assessing DNA methylation in the developing human intestinal epithelium: potential link to inflammatory bowel disease
Kraiczy, J., Nayak, K., Ross, A., Raine, T., Mak, T. N., Gasparetto, M., Cario, E., Rakyan, V. K., Heuschkel, R. B., & Zilbauer, M. (2015) · Mucosal Immunology · doi:10.1038/mi.2015.88 · Cited by 79
Epigenetic dysregulation of protocadherins in human disease
Hajj, N. E., Dittrich, M. T., & Haaf, T. (2017) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2017.07.007 · Cited by 80
Corneal cell therapy: with iPSCs, it is no more a far-sight
Chakrabarty, K., Shetty, R., & Ghosh, A. (2018) · Stem Cell Research & Therapy · doi:10.1186/s13287-018-1036-5 · Cited by 77
Can Children Catch up from the Consequences of Undernourishment? Evidence from Child Linear Growth, Developmental Epigenetics, and Brain and Neurocognitive Development
Leroy, J. L., Frongillo, E. A., Dewan, P., Black, M. M., & Waterland, R. A. (2020) · Advances in Nutrition · doi:10.1093/advances/nmaa020 · Cited by 81
“Indeed, CpG methylation is recognized as the most stable epigenetic mark (44), making it a prime candidate to mediate metabolic imprinting.”
Background
DNA Methylation: A Promising Approach in Management of Alzheimer’s Disease and Other Neurodegenerative Disorders
Kaur, G., Rathod, S. S. S., Ghoneim, M. M., Alshehri, S., Ahmad, J., Mishra, A., & Alhakamy, N. A. (2022) · Biology · doi:10.3390/biology11010090 · Cited by 79
Epigenetic regulation of the immune system in health and disease
Fernández-Morera, J. L., Calvanese, V., Rodríguez‐Rodero, S., Torre, E. L. M., & Fraga, M. F. (2010) · Tissue Antigens · doi:10.1111/j.1399-0039.2010.01587.x · Cited by 78
DNA hypomethylation of inflammation-associated genes in adipose tissue of female mice after multigenerational high fat diet feeding
Ding, Y., Li, J., Liu, S., Zhang, L., Xiao, H., Li, J., Chen, H., Petersen, R. B., Huang, K., & Zheng, L. (2014) · International Journal of Obesity · doi:10.1038/ijo.2013.98 · Cited by 76
Arabidopsis thaliana Chromosome 4 Replicates in Two Phases That Correlate with Chromatin State
Lee, T.-J., Pascuzzi, P. E., Settlage, S. B., Shultz, R. W., Tanurdžić, M., Rabinowicz, P. D., Menges, M., Zheng, P., Main, D., Murray, J. A. H., et al. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000982 · Cited by 78
“In both animals and plants, H3K4me is almost exclusively genic and correlates with gene expression [27,29,30,32,34,36,37], with H3K4me3 having the strongest positive effect on gene expression in Arabidopsis [37].”
Background
Loss of Dnmt3b function upregulates the tumor modifier Ment and accelerates mouse lymphomagenesis
Hlady, R. A., Nováková, S., Opavska, J., Klinkebiel, D. L., Peters, S. L., Bies, J., Hannah, J. D., Iqbal, J., Anderson, K. M., Siebler, H. M., et al. (2011) · Journal of Clinical Investigation · doi:10.1172/jci57292 · Cited by 79
“Basic methylation patterns are established by catalytic activity of de novo methyltransferases Dnmt3a and Dnmt3b on a demethylated genome during early embryogenesis (1).”
Background
Epigenetic regulation of endothelial‐cell‐mediated vascular repair
Fraineau, S., Palii, C. G., Allan, D., & Brand, M. (2014) · FEBS Journal · doi:10.1111/febs.13183 · Cited by 80
Anthropology Meets Epigenetics: Current and Future Directions
Thayer, Z. M., & Non, A. L. (2015) · American Anthropologist · doi:10.1111/aman.12351 · Cited by 74
Age-Related Epigenetic Drift and Phenotypic Plasticity Loss: Implications in Prevention of Age-Related Human Diseases
Li, Y., & Tollefsbol, T. O. (2016) · Epigenomics · doi:10.2217/epi-2016-0078 · Cited by 72
Differential methylation is associated with non-syndromic cleft lip and palate and contributes to penetrance effects
Alvizi, L., Ke, X., Brito, L. A., Seselgyte, R., Moore, G. E., Stanier, P., & Passos‐Bueno, M. R. (2017) · Scientific Reports · doi:10.1038/s41598-017-02721-0 · Cited by 75
DNA Demethylation in Response to Heat Stress in Arabidopsis thaliana
Korotko, U., Chwiałkowska, K., Sańko‐Sawczenko, I., & Kwaśniewski, M. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22041555 · Cited by 75
SILAC-based proteomic analysis to dissect the “histone modification signature” of human breast cancer cells
Cuomo, A., Moretti, S., Minucci, S., & Bonaldi, T. (2010) · Amino Acids · doi:10.1007/s00726-010-0668-2 · Cited by 79
“In general, the establishment of methylation patterns on H4K20, H3K27 and especially H3K9 is a complex process involving the activity of several different methyltransferases and demethylases (Cedar and Bergman 2009) To shed light, at least partial, to the molecular mechanism underlying the altered methylation patterns…”
Method
Arabidopsis RRP6L1 and RRP6L2 Function in FLOWERING LOCUS C Silencing via Regulation of Antisense RNA Synthesis
Shin, J., & Chekanova, J. A. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004612 · Cited by 75
“affecting silencing [2].”
Epigenetic Alterations and Prenatal Maternal Depression
Nemoda, Z., & Szyf, M. (2017) · Birth Defects Research · doi:10.1002/bdr2.1081 · Cited by 75
Genetic variants influence on the placenta regulatory landscape
Delahaye, F., Do, C., Kong, Y., ASHKAR, R., Salas, M. C., Tycko, B., Wapner, R. J., & Hughes, F. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007785 · Cited by 80
“between histone modification and DNA methylation (for review [58, 59]).”
Background
Whole-genome DNA methylation patterns and complex associations with gene expression associated with anthocyanin biosynthesis in apple fruit skin
Li, W., Ning, G.-X., Mao, J., Guo, Z., Zhou, Q. X., & Chen, B. (2019) · Planta · doi:10.1007/s00425-019-03266-4 · Cited by 74
Immunomodulatory Properties of Human Breast Milk: MicroRNA Contents and Potential Epigenetic Effects
Hatmal, M. M., Al-Hatamleh, M. A. I., Olaimat, A. N., Alshaer, W., Hasan, H., Albakri, K. A., Alkhafaji, E., Issa, N. N., Al‐Holy, M., Abderrahman, S. M., et al. (2022) · Biomedicines · doi:10.3390/biomedicines10061219 · Cited by 77

Authors: Cedar, H., & Bergman, Y.
Affiliations: Hebrew University of Jerusalem (IL)
Corresponding author: Cedar, Howard
ORCID: Cedar, Howard
Bergman, Yehudit
Venue: Nature Reviews Genetics
Publisher: Springer Science and Business Media LLC
Published: 2009-05
Volume: 10
Issue: 5
Pages: 295-304
ISSN: 1471-0056 (ISSN-L)
1471-0064
DOI: 10.1038/nrg2540
OpenAlex: W1976626368
Cited by: 2,267
References: 108
Citations by year: 2026: 50 · 2025: 68 · 2024: 87 · 2023: 90 · 2022: 107 · 2021: 135 · 2020: 130 · 2019: 119 · 2018: 131 · 2017: 165 · 2016: 169 · 2015: 183 · 2014: 169 · 2013: 163 · 2012: 184
FWCI: 12.31
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
Locations: Nature Reviews Genetics (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Cancer-related gene regulation
Keywords: DNA methylation, histone modifications, epigenetic crosstalk, gene repression, heterochromatin, DNA methyltransferases, chromatin structure, somatic cell reprogramming, carcinogenesis, development (biology)
MeSH terms: Histone Methyltransferases, Animals, DNA, Heterochromatin, Histones, Humans, Models, Biological, Neoplasms, Histone-Lysine N-Methyltransferase, DNA-Cytosine Methylases, DNA Methylation

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

Linking DNA methylation and histone modification: patterns and paradigms

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