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Linking DNA methylation and histone modification: patterns and paradigms
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.
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“On the other hand, the increase in scale presents computational opportunities. It allows benefitting from ‘big data’ approaches, most notably deep learning193, developed in fields such as image and text analysis, in which data sets tend to have many more samples than were available in genomics thus far.”
From Revealing the vectors of cellular identity with single-cell genomics (2016) · cites this paper as [193]
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“In addition, histone modification is a covalent post-translational modification (PTM) to histone proteins, whereas ncRNA modification occurs at the post-translational and post-transcriptional levels (Cedar and Bergman, 2009).”
BackgroundEpigenomic and enhancer dysregulation in uterine leiomyomas
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“In addition to histones, DNA also becomes methylated [40,41], an epigenetic process that has been associated with the postulated establishment of a ‘locked’, irreversible state [5].”
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“Interestingly, this relationship can work in both directions, where DNA methylation can either be directed by or be a template for histone modifications (Cedar & Bergman, 2009).”
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“Conversely, specific histone methylation can guide the establishment of DNA methylation patterns (reviewed in (15)).”
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“Certain histone methylations cause a readily reversible local formation of heterochromatin, whereas DNA methylation leads to stable long-term repression (Cedar and Bergman, 2009), especially in embryonic germ cells (Jiao et al.”
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“DNAm can have permanent effects as it leads to long‐term repression of gene expression in methylated regions of DNA.(18)”
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“Moreover, DNA methylation is highly associated with histone modifications [25], which also play an important role in epigenetic mechanisms as a result of alternating chromatin structure.”
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“In CRC patients, it has also been previously reported that reduced H3 lysine 4 methylation and increased H3 lysine 9 methylation play a critical role in the maintenance of promoter DNA methylation-associated gene silencing (15).”
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“DNA methylation may regulate gene expression through its effect on the chromatin state as well as accessibility of the transcription binding sites 3–5 and can be influenced by many pertinent environmental factors including smoking and age.”
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“The general mechanism implemented in the model follows the approach suggested by (Cedar and Bergman, 2009).”
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“Euchromatic histone-lysine N-methyltransferase 2 (EHMT2/G9a) is a major methyltransferase that catalyzes the mono-and di-methylation of histone H3 lysine 9 (H3K9me and H3K9me2) in euchromatin [14, 15].”
Direct Gingival Fibroblast/Osteoblast Transdifferentiation via Epigenetics
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“In particular, CpG island methylation represents an important epigenetic mark on the genome that is linked with histone modification and is associated with gene silencing (Cedar and Bergman 2009).”
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“Although DNA and histone methylation lead to distinguished repression of heterochromatin (stable long-term repression and local formation, respectively) [83], the crosstalk between SET domain histone methyltransferases and DNA methyltransferases is essential for relationship of both epigenetic pathways, which mediate…”
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Epigenomics of Idiopathic Pulmonary Fibrosis
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Epigenetics: A primer for clinicians
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“Histone modifications have been shown to induce DNA methylation, a process characterized during early development [85].”
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Early Postnatal Nutrition Determines Adult Physical Activity and Energy Expenditure in Female Mice
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“DNA methylation, the most stable epigenetic modification (20), is a likely mechanism to explain effects that persist for a lifetime (2).”
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“For example, decreased DNA methylation and binding of associated methyl-binding proteins is associated with impairments in histone modifications and chromatin looping [88,89].”
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“The epigenetic mechanisms of DNA methylation and histone modifications often crosstalk and influence each other.(59)”
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“The methylation of cytosines within CpG sequences, and their subsequent interaction with methyl-CpG-binding proteins (MBDs), may induce chromatin conformational modifications and inhibit the access of the transcriptional machinery to gene promoter regions, thus altering gene expression levels [100].”
BackgroundNutriepigenomics in Environmental-Associated Oxidative Stress
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“While DNA methylation is relatively stable in somatic cells, histone modifications are more diverse and dynamic, changing rapidly during the cell cycle [6,8,22,23].”
BackgroundEpigenetic reprogramming as a key contributor to melanocyte malignant transformation
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“DNA Me of CpG dinucleotides is a second major epigenetic mechanism to achieve silencing of transcription of specific genes during developmental processes (Okano et al., 1999; Cedar and Bergman, 2009).”
BackgroundCytosine methylation is a conserved epigenetic feature found throughout the phylum Platyhelminthes
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“Together, DNMTs and MBDs (complexed with other proteins [9]) comprise the core metazoan DNA methylation system found in both vertebrate and invertebrate species.”
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“In addition, changes in BAHD1 expression levels in HEK293 cells alter the patterns of H3K9 modifications and DNA methylation at the ESR1 locus, which is consistent with the interaction of BAHD1 with HDACs, KMTs, HP1 and MBD1 and the crosstalk between histone and DNAmodifications [49].”
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Novel epigenetic-sensitive clinical challenges both in type 1 and type 2 diabetes
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DNA Methylation Landscape Reflects the Spatial Organization of Chromatin in Different Cells
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“Both histone and DNA methylation play an equal important role in regulating gene expression and chromatin remodeling.(82) The balance of methylation is maintained by a group of methyltransferases and demethylases.”
BackgroundEpigenetics: New Insights into Mammary Gland Biology
Ivanova, E., Guillou, S. L., Hue‐Beauvais, C., & Provost, F. L. (2021) · Genes · doi:10.3390/genes12020231 · Cited by 47
“The crosstalk between these marks and DNA methylation plays a key role in the epigenetic regulation of genome expression [23].”
BackgroundDNA Methylation Patterning and the Regulation of Beta Cell Homeostasis
Parveen, N., & Dhawan, S. (2021) · Frontiers in Endocrinology · doi:10.3389/fendo.2021.651258 · Cited by 48
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“Recent evidence indicates that relationships between DNA methylation and histone modification have implications for understanding mechanisms of gene repression in cancer (Cedar & Bergman, 2009).”
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“…of DNA methylation and various histone modifications, which contribute to the so-called epigenetic regulatory mechanisms of gene expression, which can in turn be influenced by environmental factors and cellular signals (Cedar and Bergman, 2009; Bräutigam et al., 2013; Kinoshita and Seki, 2014).”
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“Accordingly, several studies indicate that specific histone modifications serve as marks that are used by HDACs and histone methyltransferases to recruit DNMTs and subsequently target DNA methylation to specific chromatin domains especially in de novo methylation in early development [58, 59].”
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“Genes with bivalent marks in ESCs tend to lose either H3K27-Me3 or H3K4Me3 in more differentiated, lineage-committed cells, such as the NPCs examined here (Azuara et al., 2006; Mikkelsen et al., 2007; Mohn et al., 2008; Cedar and Bergman, 2009).”
BackgroundInfluentialDNA Methylation Biphasically Regulates 3T3-L1 Preadipocyte Differentiation
Yang, X., Wu, R., Shan, W., Yu, L., Xue, B., & Shi, H. (2016) · Molecular Endocrinology · doi:10.1210/me.2015-1135 · Cited by 45
“Changes in DNA methylation have been shown to modulate histone methylation, which may act cooperatively to influence chromatin structure and thereby regulate gene expression (28).”
BackgroundPhipps, A. J., Vickers, J. C., Taberlay, P. C., & Woodhouse, A. (2016) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2016.05.003 · Cited by 48
“The location of 5mC/5hmC methylation marks on the genome has differential effects on transcription, and the outcome further depends on interplay with other epigenetic modifications such as the presence or absence of particular histone marks (Cedar and Bergman, 2009,Narayan, et al., 2015).”
BackgroundDNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications
Hong, S., & Cheng, X. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-43624-1_14 · Cited by 46
“context which is closely interwoven with DNA methylation (Hashimoto et al. 2010; Cedar and Bergman 2009).”
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Epigenetic regulation of inflammation in stroke
Ng, G. Y.-Q., Lim, Y.-A., Sobey, C. G., Dheen, S. T., Fann, D. Y., & Arumugam, T. V. (2018) · Therapeutic Advances in Neurological Disorders · doi:10.1177/1756286418771815 · Cited by 48
Yeast epigenetics: the inheritance of histone modification states
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RNF8-dependent histone ubiquitination during DNA damage response and spermatogenesis
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“The transcriptional activity of genes with CpG islands in their promoters is inversely correlated with their DNA methylation levels [27].”
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Szulwach, K. E., & Jin, P. (2013) · BioEssays · doi:10.1002/bies.201300090 · Cited by 50
“There has been a fair amount of progress in this area, leading to several core concepts about how such interactions are likely to occur more broadly [20, 84, 85].”
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Integrative modelling of tumour DNA methylation quantifies the contribution of metabolism
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The reversible effects of glial cell line–derived neurotrophic factor (GDNF) in the human brain
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FAK Activation Promotes SMC Dedifferentiation via Increased DNA Methylation in Contractile Genes
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“This observation is consistent with the results of previous studies (7, 22, 23).”
ResultRegulation of protein stability of DNA methyltransferase 1 by post-translational modifications
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“DNA methylation via DNMT1 ensures correct formation of heterochromatin [3,4] and promoter repression via histones [5].”
BackgroundSuv39h1 Mediates AP-2α-Dependent Inhibition of C/EBPα Expression during Adipogenesis
Zhang, Z.-C., Liu, Y., Li, S.-F., Guo, L., Zhao, Y., Qian, S.-W., Wen, B., Tang, Q.-Q., & Li, X. (2014) · Molecular and Cellular Biology · doi:10.1128/mcb.00070-14 · Cited by 43
Epigenetic control of thymic Treg‐cell development
Kitagawa, Y., Ohkura, N., & Sakaguchi, S. (2014) · European Journal of Immunology · doi:10.1002/eji.201444577 · Cited by 44
Wallmen, B., Schrempp, M., & Hecht, A. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks690 · Cited by 47
“One way in which promoter accessibility for Tcf/Lef proteins and Wnt target gene activation could be restricted depends on chromatin structural features (5,6).”
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A DNMT3A2-HDAC2 Complex Is Essential for Genomic Imprinting and Genome Integrity in Mouse Oocytes
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“Taken together, these results suggest a causal relationship between DNA methylation and histone modifications that is partially mediated through related histone–modifying enzymes (Cedar and Bergman, 2009).”
BackgroundZhang, Z., Zhai, Y., Ma, X., Zhang, S., An, X., Yu, H., & Li, Z. (2018) · Cellular Physiology and Biochemistry · doi:10.1159/000487579 · Cited by 44
DZNep inhibits H3K27me3 deposition and delays retinal degeneration in the rd1 mice
Zheng, S., Xiao, L., Liu, Y., Wang, Y., Cheng, L. Z., Zhang, J., Yan, N., & Chen, D. (2018) · Cell Death and Disease · doi:10.1038/s41419-018-0349-8 · Cited by 45
Epigenetic regulation of HIV-1 latency: focus on polycomb group (PcG) proteins
Khan, S., Iqbal, M., Tariq, M., Baig, S. M., & Abbas, W. (2018) · Clinical Epigenetics · doi:10.1186/s13148-018-0441-z · Cited by 46
“Though DNA methylation and histone methylation are executed by different enzymes, they maintain a close biological relationship in mediating epigenetic silencing which is further termed as double lock [62, 63].”
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“Subsequently, gene transcription is repressed by recruiting gene-silencing repressive proteins to the methylated region, such as methyl-CpG-binding protein 2 (MeCP2) and methylbinding-domain (MBD) proteins [11,12].”
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“DNA methylation and transcriptional activity have close associations with various histone modifications ( 21 , 22 ).”
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“By default, non-transformed cells are characterized by high genome-wide CpG methylation, with the exception of CpG islands (CGIs), which are mostly unmethylated [1,2,5].”
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“It has been hypothesized that DNA methylation serves as a molecular mechanism to lock in developmental changes and to determine tissue- and cellspecific functions and gene expression [42].”
BackgroundEpigenetics in the heart: the role of histone modifications in cardiac remodelling
Tingare, A., Thienpont, B., & Roderick, H. L. (2013) · Biochemical Society Transactions · doi:10.1042/bst20130012 · Cited by 42
Huisman, C., Wisman, G. B. A., Kazemier, H. G., van Vugt, M. A. T. M., van der Zee, A. G. J., Schuuring, E. M. D., & Rots, M. G. (2013) · Molecular Oncology · doi:10.1016/j.molonc.2013.02.017 · Cited by 43
Metadata
- Authors
- Cedar, H., & Bergman, Y.
- Affiliations
- Hebrew University of Jerusalem (IL)
- Corresponding author
- Cedar, Howard
- Venue
- Nature Reviews Genetics
- Published
- 2009-05
- Volume
- 10
- Issue
- 5
- Pages
- 295-304
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- 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
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