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

Show all 108 references

Sorted by citations

Items 501–600 of 1,003

A case study in cross-talk: the histone lysine methyltransferases G9a and GLP
Collins, R., & Cheng, X. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq081 · Cited by 74
Epigenetics and psychoneuroimmunology: Mechanisms and models
Mathews, H. L., & Janusek, L. W. (2010) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2010.08.009 · Cited by 77
“For a review of histone methyltransferases (see Cedar and Bergman, 2009).”
Epigenetic Modification at Notch Responsive Promoters Blunts Efficacy of Inducing Notch Pathway Reactivation After Myocardial Infarction
Felician, G., Collesi, C., Lušić, M., Martinelli, V. C., Ferro, M. D., Zentilin, L., Zacchigna, S., & Giacca, M. (2014) · Circulation Research · doi:10.1161/circresaha.115.304517 · Cited by 76
“Furthermore, in adult cardiomyocytes, the DNA sequence of these promoters shows CpG methylation, a mark of irreversible transcriptional repression.(29) We conclude that the induction of adult cardiomyocyte proliferation through Notch”
Epigenetic regulation of cardiovascular differentiation
Ohtani, K., & Dimmeler, S. (2011) · Cardiovascular Research · doi:10.1093/cvr/cvr019 · Cited by 74
Epigenetic response to environmental stress: Assembly of BRG1–G9a/GLP–DNMT3 repressive chromatin complex on Myh6 promoter in pathologically stressed hearts
Han, P., Li, W., Yang, J., Shang, C., Lin, C.-H., Cheng, W. N., Hang, C. T., Cheng, H.-L., Chen, C.-H., Wong, J., et al. (2016) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2016.03.002 · Cited by 75
Epigenetic regulation of MAGE family in human cancer progression-DNA methylation, histone modification, and non-coding RNAs
Lian, Y., Meng, L., Ding, P., & Sang, M. (2018) · Clinical Epigenetics · doi:10.1186/s13148-018-0550-8 · Cited by 78
Coordinate changes in histone modifications, mRNA levels, and metabolite profiles in clonal INS-1 832/13 β-cells accompany functional adaptations to lipotoxicity
Malmgren, S., Spégel, P., Danielsson, A. P. H., Nagorny, C. L., Andersson, L. E., Nitert, M. D., Ridderstråle, M., Mulder, H., & Ling, C. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.422527 · Cited by 71
IKKα restoration via EZH2 suppression induces nasopharyngeal carcinoma differentiation
Yan, M., Zhang, Y., He, B., Xiang, J., Wang, Z.-F., Zheng, F.-M., Xu, J., Chen, M., Zhu, Y.-L., Wen, H.-J., et al. (2014) · Nature Communications · doi:10.1038/ncomms4661 · Cited by 73
Chromatin Insulator Elements: Establishing Barriers to Set Heterochromatin Boundaries
Barkess, G., & West, A. G. (2012) · Epigenomics · doi:10.2217/epi.11.112 · Cited by 73
Cancer-Related Epigenome Changes Associated with Reprogramming to Induced Pluripotent Stem Cells
Ohm, J. E., Mali, P., Neste, L. V., Berman, D. M., Liang, L., Pandiyan, K., Briggs, K. J., Zhang, W., Argani, P., Simons, B. W., et al. (2010) · Cancer Research · doi:10.1158/0008-5472.can-10-1361 · Cited by 71
The Crucial Role of DNA Methylation and MeCP2 in Neuronal Function
Fasolino, M., & Zhou, Z. (2017) · Genes · doi:10.3390/genes8050141 · Cited by 76
“This epigenetic mark is also important in nuclear organization and compartmentalization given that the methylation of satellite repeats is an important step in the formation of heterochromatic regions [21,22].”
Background
Embryonic Temperature Programs Phenotype in Reptiles
Singh, S. K., Das, D., & Rhen, T. (2020) · Frontiers in Physiology · doi:10.3389/fphys.2020.00035 · Cited by 73
“Post-translational modifications of histones and DNA methylation are key epigenetic marks that play a part in development by regulating cell-type and tissue-specific patterns of gene expression (Cedar and Bergman, 2009; Greer and Shi, 2012).”
Background
Early nutrition and epigenetic programming: chasing shadows
Attig, L., Gabory, A., & Junien, C. (2010) · Current Opinion in Clinical Nutrition & Metabolic Care · doi:10.1097/mco.0b013e328338aa61 · Cited by 76
Integrating Early Life Experience, Gene Expression, Brain Development, and Emergent Phenotypes
Weaver, I. C. G. (2014) · Advances in genetics · doi:10.1016/b978-0-12-800222-3.00011-5 · Cited by 74
Demethylation and epigenetic modification with 5-azacytidine reduces IDH1 mutant glioma growth in combination with temozolomide
Yamashita, A. S., Rosa, M. D. C., Borodovsky, A., Festuccia, W. T., Chan, T. A.-T., & Riggins, G. J. (2018) · Neuro-Oncology · doi:10.1093/neuonc/noy146 · Cited by 73
Early life alcohol exposure primes hypothalamic microglia to later-life hypersensitivity to immune stress: possible epigenetic mechanism
Chastain, L. G., Franklin, T., Gangisetty, O., Cabrera, M. A., Mukherjee, S., Shrivastava, P., Jabbar, S., & Sarkar, D. K. (2019) · Neuropsychopharmacology · doi:10.1038/s41386-019-0326-7 · Cited by 72
Epigenetic regulation of satellite cell activation during muscle regeneration
Dilworth, F. J., & Blais, A. (2011) · Stem Cell Research & Therapy · doi:10.1186/scrt59 · Cited by 77
“DNA methylation in muscle regeneration In addition to the repressive H3K27me3 mark mediated by PRC2/Ezh2 [10], methylation of CpG dinucleotides (5-methylcytosine) within a gene regulatory region can be heritably transmitted to daughter cells to block transcription [43,44].”
Background
The role of epigenetics, particularly DNA methylation, in the evolution of caste in insect societies
Oldroyd, B. P., & Yagound, B. (2021) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2020.0115 · Cited by 69
Cytokine regulation of immune responses to Porphyromonas gingivalis
Taylor, J. J. (2010) · Periodontology 2000 · doi:10.1111/j.1600-0757.2009.00344.x · Cited by 73
“Other factors beyond genetic polymorphism contribute to interindividual variation at the genetic level; these include epigenetic factors such as DNA methylation (40), gene copy number variation (235)”
Role of ART in Imprinting Disorders
Eroğlu, A., & Layman, L. C. (2012) · Seminars in Reproductive Medicine · doi:10.1055/s-0032-1307417 · Cited by 71
Anticancer efficacy of cisplatin and trichostatin A or 5-aza-2′-deoxycytidine on ovarian cancer
Meng, F., Sun, G., Zhong, M., Yu, Y., & BREWER, M. A. (2013) · British Journal of Cancer · doi:10.1038/bjc.2013.10 · Cited by 72
Identification of a Functional Network of Human Epigenetic Silencing Factors
Poleshko, A. S., Einarson, M. B., Shalginskikh, N., Zhang, R., Adams, P. D., Skalka, A. M., & Katz, R. A. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.064667 · Cited by 73
mRNA imprinting
Choder, M. (2011) · Cellular Logistics · doi:10.4161/cl.1.1.14465 · Cited by 72
“Epigenetic studies focus on DNA and chromatin.(31) Recently this concept has been broadened to include also no -coding RNAs and association of components of transcriptional regulatory machinery with target genes on mitotic chromosomes.”
Maternal obesity and prenatal programming
Elshenawy, S., & Simmons, R. A. (2016) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2016.07.002 · Cited by 72
“Recent evidence indicates that this reciprocal relationship between histone methylation and DNA methylation might be accomplished by direct interactions between histone and DNA methyltransferases [27].”
Background
Preclinical models for obesity research
Barrett, P., Mercer, J. G., & Morgan, P. J. (2016) · Disease Models & Mechanisms · doi:10.1242/dmm.026443 · Cited by 78
Epigenetic Changes in Endothelial Progenitors as a Possible Cellular Basis for Glycemic Memory in Diabetic Vascular Complications
Rajasekar, P., O’Neill, C. L., Eeles, L., Stitt, A. W., & Medina, R. J. (2015) · Journal of Diabetes Research · doi:10.1155/2015/436879 · Cited by 71
“It has been established that there exists a crosstalk between PTHMs and DNA methylation and that they are highly interdependent in determining gene expression status [73].”
Background
Genome-wide methylation analyses of primary human leukocyte subsets identifies functionally important cell-type–specific hypomethylated regions
Zilbauer, M., Rayner, T. F., Clark, C., Coffey, A. J., Joyce, C. J., Palta, P., Palotie, A. V., Lyons, P., & Smith, K. G. C. (2013) · Blood · doi:10.1182/blood-2013-05-503201 · Cited by 71
MUC1-C activates polycomb repressive complexes and downregulates tumor suppressor genes in human cancer cells
Rajabi, H. N., Hiraki, M., & Kufe, D. W. (2018) · Oncogene · doi:10.1038/s41388-017-0096-9 · Cited by 71
Pathogenesis of Human Adenomyosis: Current Understanding and Its Association with Infertility
Khan, K. N., Fujishita, A., & Mori, T. (2022) · Journal of Clinical Medicine · doi:10.3390/jcm11144057 · Cited by 77
“A family of enzymes, such as deoxyribonucleic acid methytransferases (DNMTs), catalyze transfer of a methyl group to DNA, resulting in more compact chromatin and hence gene repression [44,45].”
Background
Epigenetic dysregulation in glioma
Kondo, Y., Katsushima, K., Ohka, F., Natsume, A., & Shinjo, K. (2014) · Cancer Science · doi:10.1111/cas.12379 · Cited by 73
Histone H3K9 modifications are a local chromatin event involved in ethanol-induced neuroadaptation of the NR2B gene
Qiang, M., Denny, A. D., Lieu, M., Carreon, S., & Li, J. (2011) · Epigenetics · doi:10.4161/epi.6.9.16924 · Cited by 72
Role of epigenetic mechanisms in the development of chronic complications of diabetes
Wegner, M., Neddermann, D., Pioruńska-Stolzmann, M., & Jagodziński, P. P. (2014) · Diabetes Research and Clinical Practice · doi:10.1016/j.diabres.2014.03.019 · Cited by 72
“[45] Cedar H, Bergman Y.”
Background
MicroRNAs and DNA methylation as epigenetic regulators of mitosis, meiosis and spermiogenesis
Yao, C., Liu, Y., Sun, M., Niu, M., Yuan, Q., Hai, Y., Guo, Y., Chen, Z., Hou, J., Liu, Y., et al. (2015) · Reproduction · doi:10.1530/rep-14-0643 · Cited by 73
“This strategy is unstable and the silenced genes can be reactivated under certain circumstances (Cedar & Bergman 2009).”
Exercise training alters DNA methylation patterns in genes related to muscle growth and differentiation in mice.
Kanzleiter, T., Jähnert, M., Schulze, G., Selbig, J., Hallahan, N., Schwenk, R., & Schürmann, A. (2015) · American Journal of Physiology. Endocrinology and Metabolism · doi:10.1152/ajpendo.00289.2014 · Cited by 57
Methylation analyses in liquid biopsy
Lissa, D., & Robles, A. I. (2016) · Translational Lung Cancer Research · doi:10.21037/tlcr.2016.10.03 · Cited by 71
The mutational spectrum of non-CpG DNA varies with CpG contentPreprint
Walser, J., & Furano, A. V. (2010) · Genome Research · doi:10.1101/gr.103283.109 · Cited by 75
“In either case, methyl-CpGmaymediate the recruitment of various DNA- or histone-binding proteins andother factors (Martens et al. 2005; Cedar and Bergman 2009), which could conceivably affect the susceptibility of the DNA to mutation.”
Background
Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b
Ebata, K. T., Mesh, K., Liu, S., Bilenky, M., Fekete, A., Acker, M. G., Hirst, M., Garcia, B. A., & Ramalho‐Santos, M. (2017) · Epigenetics & Chromatin · doi:10.1186/s13072-017-0143-3 · Cited by 72
“There is extensive crosstalk between DNA methylation and histone methylation [17].”
Environmental change and the evolution of genomes: Transposable elements as translators of phenotypic plasticity into genotypic variability
Pimpinelli, S., & Piacentini, L. (2019) · Functional Ecology · doi:10.1111/1365-2435.13497 · Cited by 79
Bisulfite-Converted DNA Quantity Evaluation: A Multiplex Quantitative Real-Time PCR System for Evaluation of Bisulfite Conversion
Hong, S. R., & Shin, K. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.618955 · Cited by 70
“, 2019), development (Cedar and Bergman, 2009), and diseases (Greenberg and Bourc’his, 2019).”
Background
The Role of DNMT Methyltransferases and TET Dioxygenases in the Maintenance of the DNA Methylation Level
Davletgildeeva, A. T., & Kuznetsov, N. A. (2024) · Biomolecules · doi:10.3390/biom14091117 · Cited by 76
“It was demonstrated not so long ago that the methylation of DNA and methylation of histones can synergistically regulate chromatin structure and function [93–95].”
Background
Epigenetic Silencing of miRNA-34a in Human Cholangiocarcinoma via EZH2 and DNA Methylation
Kwon, H., Song, K., Han, C., Zhang, J., Lu, L., Chen, W., & Wu, T. (2017) · American Journal Of Pathology · doi:10.1016/j.ajpath.2017.06.014 · Cited by 71
Parental diet, pregnancy outcomes and offspring health: metabolic determinants in developing oocytes and embryos
Sinclair, K. D., & Watkins, A. J. (2013) · Reproduction Fertility and Development · doi:10.1071/rd13290 · Cited by 76
“…studied, although it recognised that the establishment and erasure of DNA methylation marks within CpG dinucleotides 285 is carefully orchestrated to coincide with covalent modifications to associated histone complexes in an inter-dependent manner during early development (Cedar and Bergman, 2009).”
Background
A survey of inter-individual variation in DNA methylation identifies environmentally responsive co-regulated networks of epigenetic variation in the human genome
Garg, P., Joshi, R. S., Watson, C. T., & Sharp, A. J. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007707 · Cited by 73
Mechanistic Basis for Maintenance of CHG DNA Methylation in Plants
Fang, J., Jiang, J., Leichter, S. M., Liu, J., Biswal, M., Khudaverdyan, N., Zhong, X., & Song, J. (2022) · Nature Communications · doi:10.1038/s41467-022-31627-3 · Cited by 69
Histone Modification Therapy of Cancer
Biancotto, C., Frigè, G., & Minucci, S. (2010) · Advances in genetics · doi:10.1016/b978-0-12-380866-0.60013-7 · Cited by 74
Inhibition of G9a induces DUSP4-dependent autophagic cell death in head and neck squamous cell carcinoma
Li, K., Hua, K., Lin, Y.-S., Su, C., Ko, J., Hsiao, M., Kuo, M., & Tan, C. (2014) · Molecular Cancer · doi:10.1186/1476-4598-13-172 · Cited by 69
“Among different states of histone modification, methylation is generally considered an important mechanism for regulating gene expression and chromosome organization that may contribute to development and maintenance of physiological functions [4,5].”
Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences
Yegnasubramanian, S., Wu, Z. J., Haffner, M. C., Esopi, D., Aryee, M. J., Badrinath, R., He, T. L., Morgan, J., Carvalho, B. S., Zheng, Q., et al. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-313 · Cited by 69
“Methylation at the 5-position of cytosine in CpG dinucleotides is a key epigenetic process in vertebrate species where it serves critical roles in normal genome homeostasis, including transcriptional regulation, establishment of chromatin structure, suppression of repetitive elements, imprinting, and × chromosome inac…”
Background
An epigenetic switch regulatesde novoDNA methylation at a subset of pluripotency gene enhancers during embryonic stem cell differentiation
Petell, C. J., AlAbdi, L., He, M., Miguel, P. S., Rose, R., & Gowher, H. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw426 · Cited by 66
“Given that several studies have described the relationship between histone deacetylation and DNA methylation (16), we investigated the contribution of Lsd1 activity in regulating DNA methylation by Dnmt3a at PpG enhancers during ESC differentiation.”
Background
Mechanical stimulation promote the osteogenic differentiation of bone marrow stromal cells through epigenetic regulation of Sonic Hedgehog
Wang, C., Shan, S., Wang, C., Wang, J., Li, J., Hu, G., Dai, K., Li, Q., & Zhang, X. (2017) · Experimental Cell Research · doi:10.1016/j.yexcr.2017.02.021 · Cited by 69
Histone deacetylases (HDACs) as therapeutic target for depressive disorders
Misztak, P., Pańczyszyn-Trzewik, P., & Sowa-Kućma, M. (2017) · Pharmacological Reports · doi:10.1016/j.pharep.2017.08.001 · Cited by 73
Epigenetic silencing of genes enhanced by collective role of reactive oxygen species and MAPK signaling downstream ERK/Snail axis: Ectopic application of hydrogen peroxide repress CDH1 gene by enhanced DNA methyltransferase activity in human breast cancer
Pradhan, N., Parbin, S., Kar, S., Das, L., Kirtana, R., Seshadri, G. S., Sengupta, D., Deb, M., Kausar, C., & Patra, S. K. (2019) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2019.04.002 · Cited by 69
HERES, a lncRNA that regulates canonical and noncanonical Wnt signaling pathways via interaction with EZH2
Yu, B., Yoon, J.-H., Kang, H., Lee, E. K., Lee, S. K., & Nam, J. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1912126116 · Cited by 71
Regulating microRNA expression: at the heart of diabetes mellitus and the mitochondrion
Hathaway, Q. A., Pinti, M. V., Durr, A. J., Waris, S. A., Shepherd, D. L., & Hollander, J. M. (2017) · American Journal of Physiology-Heart and Circulatory Physiology · doi:10.1152/ajpheart.00520.2017 · Cited by 69
“What are epigenetics? The most described forms of epigenetic regulation consist primarily of two transient alterations: DNA methylation and histone modification (21).”
Background
Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains
Jensen, T. J., Kim, S. K., Zhu, Z., Chin, C. L., Gebhard, C., Lu, T. T., Deciu, C., van den Boom, D., & Ehrich, M. (2015) · Genome biology · doi:10.1186/s13059-015-0645-x · Cited by 68
“Differences in DNA methylation patterns are cell type specific and, in concert with histone tail modifications and other epigenetic alterations, cooperate to modulate chromatin structure [14-17].”
Background
Genome-wide DNA methylation analysis identifies a metabolic memory profile in patient-derived diabetic foot ulcer fibroblasts
Park, L. K., Maione, A. G., Smith, A., Gerami‐Naini, B., Iyer, L. K., Mooney, D. J., Veves, A., & Garlick, J. A. (2014) · Epigenetics · doi:10.4161/15592294.2014.967584 · Cited by 73
“Interpreting genome-wide epigenomic data relies on analyzing the interdependency of DNA methylation and histone modification patterns that cooperatively determine transcriptional activity.(54,55) Previous studies in the context of cancer(56) and cell differentiation(57) have identified DNA methylation patterns and his…”
The high mobility group A2 protein epigenetically silences the Cdh1 gene during epithelial-to-mesenchymal transition
Tan, E., Kahata, K., Idås, O., Thuault, S., Heldin, C., & Moustakas, A. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1293 · Cited by 68
“Tri-methylation of lysine 4 (H3K4me3) and acetylation of lysine 9 (H3K9ac) residues in histone H3 are associated with gene transcription, whereas tri-methylation of lysine 9 (H3K9me3) and lysine 27 (H3K27me3) residues are markers of gene repression (7).”
Influential
Computations Reveal a Rich Mechanistic Variation of Demethylation of N-Methylated DNA/RNA Nucleotides by FTO
Wang, B., Cao, Z., Sharon, D. A., & Shaik, S. S. (2015) · ACS Catalysis · doi:10.1021/acscatal.5b01867 · Cited by 69
Contribution of Neuroepigenetics to Huntington’s Disease
Francelle, L., Lotz, C., Outeiro, T. F., Brouillet, E., & Mérienne, K. (2017) · Frontiers in Human Neuroscience · doi:10.3389/fnhum.2017.00017 · Cited by 73
“Activation of specific signaling pathways, such as the cAMP/CREB/CREBbinding protein (CBP) pathway, is involved in the coupling between epigenetic and transcriptional responses, promoting the recruitment of protein complexes at target genes, which induces chromatin remodeling and drive transcription (Cedar and Bergman…”
Background
Epigenetic Guardian: A Review of the DNA Methyltransferase DNMT3A in Acute Myeloid Leukaemia and Clonal Haematopoiesis
Chaudry, S. F., & Chevassut, T. J. T. (2017) · BioMed Research International · doi:10.1155/2017/5473197 · Cited by 69
“One example of this is histone modiiers, such as H3K9 methyltransferase enzyme, which are observed to interact with DNMT3A [52], though the signiicance in respect to methylation activity is not well understood.”
Background
A Concise Review on Epigenetic Regulation: Insight into Molecular Mechanisms
Golbabapour, S., Abdulla, M. A., & Hajrezaei, M. (2011) · International Journal of Molecular Sciences · doi:10.3390/ijms12128661 · Cited by 72
“Reinforcement of epigenetic states happens through mutual relationship between DNA methylation and histone modifications [34].”
Background
Causes and Consequences of Age-Related Changes in DNA Methylation: A Role for ROS?
Rang, F. J., & Boonstra, J. (2014) · Biology · doi:10.3390/biology3020403 · Cited by 65
“Notably, it is known that an intricate interplay exists between histone modifications and DNA methylation (see [125]).”
Background
Stable transmission of reversible modifications: maintenance of epigenetic information through the cell cycle
Blomen, V. A., & Boonstra, J. (2010) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-010-0505-5 · Cited by 73
Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics
Aguilar, C. A., & Craighead, H. G. (2013) · Nature Nanotechnology · doi:10.1038/nnano.2013.195 · Cited by 67
The EBNA3 Family: Two Oncoproteins and a Tumour Suppressor that Are Central to the Biology of EBV in B Cells
Allday, M. J., Bazot, Q., & White, R. E. (2015) · Current topics in microbiology and immunology · doi:10.1007/978-3-319-22834-1_3 · Cited by 71
Developmental programming: State‐of‐the‐science and future directions–Summary from a Pennington Biomedical symposium
Sutton, E. F., Gilmore, L. A., Dunger, D. B., Heijmans, B. T., Hivert, M., Ling, C., Martínez, J. A., Ozanne, S. E., Simmons, R. A., Szyf, M., et al. (2016) · Obesity · doi:10.1002/oby.21487 · Cited by 72
“On the other hand, DNA methylation, which occurs in mammals predominantly at CpG dinucleotides, can be stably maintained due to the semiconservative replication of CpG methylation during mitosis via the action of the maintenance methylase DNMT1 (70).”
Background
Epigenetic Modifications and Therapy in Multiple Sclerosis
Aslani, S., Jafari, N., Javan, M. R., Karami, J., Ahmadi, M., & Jafarnejad, M. (2016) · NeuroMolecular Medicine · doi:10.1007/s12017-016-8422-x · Cited by 69
Epigenetic mechanisms of macrophage activation in type 2 diabetes
Ahmed, M., de Winther, M. P. J., & den Bossche, J. V. (2016) · Immunobiology · doi:10.1016/j.imbio.2016.08.011 · Cited by 67
Inhibition of demethylase KDM6B sensitizes diffuse large B-cell lymphoma to chemotherapeutic drugs
Mathur, R., Sehgal, L., Havránek, O., Köhrer, S., Khashab, T., Jain, N. K., Burger, J. A., Neelapu, S. S., Davis, R. E., & Samaniego, F. (2016) · Haematologica · doi:10.3324/haematol.2016.144964 · Cited by 67
“Histone methylation governs the outcomes of epigenetic reprogramming during B-cell activation and memory B-cell generation.(16,17) Aberrant histone methylation or demethylation can result in inappropriate transcriptional silencing, which can drive chemoresistance and malignant transformation.”
Background
Foodomics for human health: current status and perspectives
Braconi, D., Bernardini, G., Millucci, L., & Santucci, A. (2017) · Expert Review of Proteomics · doi:10.1080/14789450.2018.1421072 · Cited by 71
Latent Regulatory Potential of Human-Specific Repetitive Elements
Ward, M. C., Wilson, M. D., Barbosa‐Morais, N. L., Schmidt, D., Stark, R., Pan, Q., Schwalie, P. C., Menon, S., Lukk, M., Watt, S., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.11.013 · Cited by 66
“Indeed, cytosine methylation is typically anticorrelated with H3K4me3 (Cedar and Bergman, 2009).”
Background
Cadmium Induces Histone H3 Lysine Methylation by Inhibiting Histone Demethylase Activity
Xiao, C., Liu, Y., Xie, C., Tu, W., Xia, Y., Costa, M., & Zhou, X. M. (2015) · Toxicological Sciences · doi:10.1093/toxsci/kfv019 · Cited by 66
“In general, DNA methylation may act as a template for some histone modifications following DNA replication but more likely histone methylation can aid in directing DNA methylation patterns (Cedar and Bergman, 2009).”
Background
Correlated 5-Hydroxymethylcytosine (5hmC) and Gene Expression Profiles Underpin Gene and Organ-Specific Epigenetic Regulation in Adult Mouse Brain and Liver
Lin, I., Chen, Y., & Hsu, M. (2017) · PLoS ONE · doi:10.1371/journal.pone.0170779 · Cited by 69
Towards ageing well: Use it or lose it: Exercise, epigenetics and cognition
Rea, I. M. (2017) · Biogerontology · doi:10.1007/s10522-017-9719-3 · Cited by 76
“…for the genes and the addition or removal these tags by methylation/demethylation, acetylation/deacetylation or phosphorylation/dephosphorylation, (Cedar and Bergman 2009), allow gene expression and activity to be fine-tuned and rapidly modified in response to environmental triggers such as…”
Background
Perspectives on the Role of Histone Modification in Breast Cancer Progression and the Advanced Technological Tools to Study Epigenetic Determinants of Metastasis
Zhuang, J., Huo, Q., Yang, F., & Xie, N. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.603552 · Cited by 67
Histone methyltransferase SETDB1 is required for prostate cancer cell proliferation, migration and invasion
Ying-hao, S. U. N., Sun, Y., Wei, M., Ren, S., Chen, R., Xu, W., Wang, F., Lu, J., Shen, J. G., Yu, Y.-W., et al. (2014) · Asian Journal of Andrology · doi:10.4103/1008-682x.122812 · Cited by 64
Leptin resistance and obesity in mice with deletion of methyl-CpG-binding protein 2 (MeCP2) in hypothalamic pro-opiomelanocortin (POMC) neurons
Wang, X., Lacza, Z., Sun, Y. E., & Han, W. (2013) · Diabetologia · doi:10.1007/s00125-013-3072-0 · Cited by 67
“As histone methylation and DNA methylation reciprocally influence each other [47], increased dimethylated H3K9 may lead to a higher level of DNA methylation, resulting in a closed inactive chromatin conformation and further reduction of Pomc expression.”
Lysine demethylase KDM2A inhibits TET2 to promote DNA methylation and silencing of tumor suppressor genes in breast cancer
Chen, J.-Y., Luo, C.-W., Lai, Y.-S., Wu, C., & Hung, W. (2017) · Oncogenesis · doi:10.1038/oncsis.2017.71 · Cited by 65
Crosstalk Between Histone and DNA Methylation in Regulation of Retinal Matrix Metalloproteinase-9 in Diabetes
Duraisamy, A. J., Mishra, M., & Kowluru, R. A. (2017) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.17-22706 · Cited by 70
“For example, histone methylation can direct DNA methylation patterns, and DNA methylation can serve as a template for some histone modifications after DNA replication.(40) H3K27me3 itself is a repressive mark associated with gene repression,(41) but Ezh2 can also control DNA methylation directly by regulating Dnmts.”
Background
Caloric restriction mitigates age-associated hippocampal differential CG and non-CG methylation
Hadad, N., Unnikrishnan, A., Jackson, J. A., Masser, D. R., Otalora, L., Stanford, D. R., Richardson, A. G., & Freeman, W. M. (2018) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2018.03.009 · Cited by 66
Developmental Epigenetics: Phenotype and the Flexible Epigenome
John, R. M., & Rougeulle, C. (2018) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2018.00130 · Cited by 68
“From a molecular view, classic epigenetic marks include DNA methylation and the modification of proteins that lie on or over the DNA sequence itself (Cedar and Bergman, 2009).”
Background
DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.)
Zakrzewski, F., Schmidt, M. U., Lijsebettens, M. V., & Schmidt, T. (2017) · The Plant Journal · doi:10.1111/tpj.13526 · Cited by 67
“Relationships between DNA methylation and histone modification have implications for normal development and somatic cell reprogramming (Cedar and Bergman, 2009).”
Background
Upregulation of Ets1 expression by NFATc2 and NFKB1/RELA promotes breast cancer cell invasiveness
Kim, G.-C., Kwon, H., Lee, C., Verma, R. P., Rudra, D., Kim, T., Kang, K., Nam, J. H., Kim, Y., & Im, S. (2018) · Oncogenesis · doi:10.1038/s41389-018-0101-3 · Cited by 67
Regulation of cytochrome P450 expression by microRNAs and long noncoding RNAs: Epigenetic mechanisms in environmental toxicology and carcinogenesis
Li, D., Tolleson, W. H., Yu, D., Chen, S., Guo, L., Xiao, W., Tong, W., & Ning, B. (2019) · Journal of Environmental Science and Health Part C · doi:10.1080/10590501.2019.1639481 · Cited by 64
Differences in network controllability and regional gene expression underlie hallucinations in Parkinson’s disease
Zarkali, A., McColgan, P., Ryten, M., Reynolds, R. H., Leyland, L., Lees, A. J., Rees, G. E., & Weil, R. S. (2020) · Brain · doi:10.1093/brain/awaa270 · Cited by 58
“Histone methylation is important for transcriptional control (Greer and Shi, 2012) and closely related to DNA methylation (Cedar and Bergman, 2009), which is a hallmark of ageing, predicting lifespan (Hannum et al.”
Background
Aberrant DNA methylation associated with aggressiveness of gastrointestinal stromal tumour
Okamoto, Y., Sawaki, A., Ito, S., Nishida, T., Takahashi, T., Toyota, M., Suzuki, H., Shinomura, Y., Takeuchi, I., Shinjo, K., et al. (2011) · Gut · doi:10.1136/gut.2011.241034 · Cited by 64
“It seems that CpG islands targeted by aberrant DNA methylation in malignant cells are determined by a preprogrammed targeting mechanism.(40) Studies have demonstrated that the existence of stalled or active RNA polymerase II (Pol II) on promoter regions might be a cue to determine the epigenetic fate of promoter DNA m…”
Background
Metformin inhibits SUV39H1-mediated migration of prostate cancer cells
Yu, T., Wang, C., Yang, J., Guo, Y., Wu, Y., & Li, X. (2017) · Oncogenesis · doi:10.1038/oncsis.2017.28 · Cited by 64
A genome-wide DNA methylation signature for SETD1B-related syndrome
Krzyzewska, I. M., Maas, S. M., Henneman, P., van der Lip, K., Venema, A., Baranano, K. W., Chassevent, A., Aref‐Eshghi, E., van Essen, A. J., Fukuda, T., et al. (2019) · Clinical Epigenetics · doi:10.1186/s13148-019-0749-3 · Cited by 64
Genetic and epigenetic regulation of skeletal muscle ribosome biogenesis with exercise
Figueiredo, V. C., Wen, Y., Alkner, B., Fernandez‐Gonzalo, R., Norrbom, J., Vechetti, I. J., Valentino, T., Mobley, C. B., Zentner, G. E., Peterson, C. A., et al. (2021) · The Journal of Physiology · doi:10.1113/jp281244 · Cited by 64
“There is a strong interrelationship between chromatin modifications and DNA methylation (Eden et al., 1998; Fuks, 2005; Nemeth et al., 2008; Cedar & Bergman, 2009), so published chromatin immunoprecipitation (ChIP) and rDNA mapping data (Grandori et al., 2005; Zentner et al., 2011a; Shiue et al.,…”
Background
Hope for Restoration of Dead Valuable Bulls through Cloning Using Donor Somatic Cells Isolated from Cryopreserved Semen
Selokar, N. L., Saini, M., Palta, P., Chauhan, M. S., Manik, R. S., & Singla, S. K. (2014) · PLoS ONE · doi:10.1371/journal.pone.0090755 · Cited by 63
“DNA methylation is a widely accepted gene expression silencing mark and is considered as being coupled to H3K27me3 through enzymatic interaction [21].”
Background
TFIIH Subunit Alterations Causing Xeroderma Pigmentosum and Trichothiodystrophy Specifically Disturb Several Steps during Transcription
Singh, A., Compe, E., May, N. L., & Egly, J. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.12.012 · Cited by 63
Epigenetic Silencing Mediated through Activated PI3K/AKT Signaling in Breast Cancer
Zuo, T., Liu, T.-M., Lan, X., Weng, Y., Shen, R. Z., Gu, F., Huang, Y., Liyanarachchi, S., Deatherage, D. E., Hsu, P.-Y., et al. (2011) · Cancer Research · doi:10.1158/0008-5472.can-10-3573 · Cited by 63
The Effect of DNA CpG Methylation on the Dynamic Conformation of a Nucleosome
Jimenez‐Useche, I., & Yuan, C. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.11.012 · Cited by 63
Transgenerational epigenetic inheritance: Focus on soma to germline information transfer
Sharma, A. (2012) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2012.12.003 · Cited by 65
Nutrient-driven O-GlcNAc cycling – think globally but act locally
Harwood, K. R., & Hanover, J. A. (2014) · Journal of Cell Science · doi:10.1242/jcs.113233 · Cited by 63
“cytosine by DNA methyltransferases, termed 5-methylcytosine or 5-mC, generally results in gene repression (Cedar and Bergman, 2009; Suzuki and Bird, 2008).”
Background
Epigenetic disruption and glucose homeostasis changes following low-dose maternal bisphenol A exposure
Chang, H., Wang, D., Xia, W., Pan, X., Huo, W., Xu, S., & Li, Y. (2016) · Toxicology Research · doi:10.1039/c6tx00047a · Cited by 62
The Histone Methyltransferase G9a Promotes Cholangiocarcinogenesis Through Regulation of the Hippo Pathway Kinase LATS2 and YAP Signaling Pathway
Ma, W., Han, C., Zhang, J., Song, K., Chen, W., Kwon, H., & Wu, T. (2020) · Hepatology · doi:10.1002/hep.31141 · Cited by 62
“Some well-characterized cancer epigenetic changes include posttranslational modifications of histone proteins, which are known to regulate the loosening of the nucleosome, affecting the binding of transcription factors and RNA polymerase to their target genes.(37,38) As one of the most well-studied patterns among hist…”
Background
The role of NSD1, NSD2, and NSD3 histone methyltransferases in solid tumors
Topchu, I., Pangeni, R. P., Bychkov, I., Miller, S. A., Izumchenko, E., Yu, J., Golemis, E. A., Karanicolas, J., & Boumber, Y. (2022) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-022-04321-2 · Cited by 64
“KMTs, including SET domain-containing proteins, influence de novo DNA methylation during embryonic development by recruiting DNA methyltransferases (DNMTs) [117].”
The P olycomb group protein MEDEA and the DNA methyltransferase MET 1 interact to repress autonomous endosperm development in A rabidopsis
Schmidt, A., Wöhrmann, H. J. P., Raissig, M. T., Arand, J., Gheyselinck, J., Gagliardini, V., Heichinger, C., Walter, J., & Grossniklaus, U. (2012) · The Plant Journal · doi:10.1111/tpj.12070 · Cited by 62
Epigenetic Modifications and Canonical Wingless/int-1 Class (WNT) Signaling Enable Trans-differentiation of Nonosteogenic Cells into Osteoblasts
Cho, Y. D., Yoon, W. J., Kim, W. J., Woo, K. M., Baek, J. H., Lee, G., Ku, Y., van Wijnen, A. J., & Ryoo, H. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.558064 · Cited by 62
“Epigenetic Protein Modifications on Histone H3 Parallel Changes in DNA Methylation and Gene Expression—Changes in CpG methylation are functionally interrelated with histone modifications and control of promoter accessibility in chromatins that mediate silencing or activation of gene transcription (30).”
Background
Epigenetic programming of hypoxic–ischemic encephalopathy in response to fetal hypoxia
Ma, Q., & Zhang, L. (2014) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2014.11.001 · Cited by 63

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