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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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Linking the Epigenome with Exposure Effects and Susceptibility: The Epigenetic Seed and Soil Model
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BackgroundInfluentialKDM5c inhibits multidrug resistance of colon cancer cell line by down-regulating ABCC1
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“In the DNMT-catalysed reactions, S-adenosylmethionine (SAM) is the donor of methyl group which is associated to gene repression by two major mechanisms: (1) it obstacles the binding of transcription factors (activators) to their specific sites; (2) it recruits methyl-CpG-binding proteins, such as MECP2 or MBD2 which,…”
BackgroundEpigenetic Changes Associated With Exposure to Glyphosate-Based Herbicides in Mammals
Rossetti, M. F., Canesini, G., Lorenz, V., Milesi, M. M., Varayoud, J., & Ramos, J. G. (2021) · Frontiers in Endocrinology · doi:10.3389/fendo.2021.671991 · Cited by 41
Dyson, M. T., Kakinuma, T., Pavone, M. E., Monsivais, D., Navarro, A., Malpani, S. S., Ono, M., & Bulun, S. E. (2015) · Fertility and Sterility · doi:10.1016/j.fertnstert.2015.06.046 · Cited by 37
Hing, B., Gardner, C., & Potash, J. B. (2014) · American Journal of Medical Genetics Part B: Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32265 · Cited by 47
“This is due to the ability of DNA methylation to regulate gene expression by regulating accessibility of transcription factors to their binding sites and influencing chromatin structure (Watt and Molloy, 1988; Iguchi-Ariga and Schaffner, 1989; Cedar and Bergman, 2009).”
BackgroundHicks, K., & Leonard, W. R. (2014) · Current Anthropology · doi:10.1086/678055 · Cited by 37
“…how early-life environments produce biological changes that can be transmitted across generations, and a number of recent studies have addressed the role of DNA methylation in shaping human phenotypes (Cedar and Bergman 2009; Dominguez-Salas et al. 2013; Kuzawa 2013; Waterland and Michels 2007).”
BackgroundGenomic Approaches to Deconstruct Pluripotency
Loh, Y., Yang, L., Yang, J. C., Li, H., Collins, J. J., & Daley, G. Q. (2011) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082410-101506 · Cited by 37
Impact of the Exposome on the Epigenome in Inflammatory Bowel Disease Patients and Animal Models
Vieujean, S., Caron, B., Haghnejad, V., Jouzeau, J., Netter, P., Heba, A.-C., Ndiaye, N. C., Moulin, D., Barreto, G., Danese, S., et al. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23147611 · Cited by 41
“While DNA methylation is relatively stable in somatic cells, histone modifications are more diverse and dynamic, changing rapidly during the course of the cell cycle [6,30,53,54].”
BackgroundWhole genome methylation analyses of schizophrenia patients before and after treatment
Rukova, B. B., Staneva, R., Hadjidekova, S. P., Stamenov, G., Milanova, V. K., & Toncheva, D. I. (2014) · Biotechnology & Biotechnological Equipment · doi:10.1080/13102818.2014.933501 · Cited by 37
“brain diseases.[11,12] There is literature data about involvement of some psychiatric drugs in epigenetic”
BackgroundEpigenetics and fetal adaptation to perinatal events: Diversity through fidelity1
Joss‐Moore, L. A., Metcalfe, D. B., Albertine, K. H., McKnight, R. A., & Lane, R. H. (2009) · Journal of Animal Science · doi:10.2527/jas.2009-2352 · Cited by 37
“It is also interesting to consider that DNA methylation and histone modifications appear to act in a coordinated fashion (Cedar and Bergman, 2009).”
BackgroundDynamic epigenetic responses to muscle contraction.
Rasmussen, M., Zierath, J., & Barrès, R. (2014) · Drug Discovery Today · doi:10.1016/j.drudis.2014.03.003 · Cited by 39
DNA Methylation and Chromatin Organization in Insects: Insights from the Ant Camponotus floridanus
Glastad, K. M., Hunt, B. G., & Goodisman, M. A. D. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv039 · Cited by 36
“…Modifications Recent studies in plants (Zilberman et al. 2008; Zemach et al. 2010; Coleman-Derr and Zilberman 2012) and animals (Ooi et al. 2007; Cedar and Bergman 2009; Shukla et al. 2011) have demonstrated that epigenetic information encoded by DNA methylation and hPTMs may interact to affect…”
BackgroundSun, W., Zhou, X., Zheng, J., Lu, M., Nie, J.-Y., Yang, X., & Zheng, Z. (2011) · Acta Biochimica et Biophysica Sinica · doi:10.1093/abbs/gmr113 · Cited by 40
Epigenetic regulation of TGF-β1 signalling in dilative aortopathy of the thoracic ascending aorta
Forte, A., Galderisi, U., Cipollaro, M., FEO, M. D., & Corte, A. D. (2016) · Clinical Science · doi:10.1042/cs20160222 · Cited by 37
Epigenetic mechanism and target therapy of UHRF1 protein complex in malignancies
Xue, B., Zhao, J., Feng, P., Xing, J., Wu, H., & Li, Y. (2019) · OncoTargets and Therapy · doi:10.2147/ott.s192234 · Cited by 38
“and HDAC1 can deacetylate DNMT1 to protect it from degradation.(64,77) In addition, the stability of DNMT1 is”
BackgroundEZH2: An Accomplice of Gastric Cancer
Yu, W., Liu, N., Song, X., Chen, L., Wang, M., Xiao, G., Li, T., Wang, Z., & Zhang, Y. (2023) · Cancers · doi:10.3390/cancers15020425 · Cited by 37
“In addition, DNA methylation might serve as a template for some histone modifications after DNA replication [29].”
BackgroundFan, D., Dai, Y., Wang, X., Wang, Z., He, H., Yang, H., Cao, Y., Deng, X. W., & Ma, L. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks647 · Cited by 37
“Besides the interaction between siRNAs andDNAmethylation, histone H3K9 methylation, an epigenetic marker of transcriptional inactivation, is highly associated with DNA methylation in plants and animals (19).”
Ng, C., Aichinger, M., Nguyen, T. H., Au, C., Najar, T. A., Wu, L., Mesa, K. R., Liao, W., Quivy, J., Hubert, B., et al. (2019) · Genes & Development · doi:10.1101/gad.322024.118 · Cited by 37
“Thus, the study of the Cd4 locus represents an attractive system to understand how DNA methylation and other epigenetic modifications may cooperate to regulate transcriptional memory, an integral component of vertebrate development (Cedar and Bergman 2009).”
Kostaki, M., Manona, A. D., Stavraka, I., Korkolopoulou, P. A., Levidou, G., Trigka, E., Christofidou, E., Champsas, G., Stratigos, A., Katsambas, A., et al. (2014) · Experimental Dermatology · doi:10.1111/exd.12398 · Cited by 36
Epigenetic inactivation of DNA repair in breast cancer
Nowsheen, S., Aziz, K., Tran, P. T., Gorgoulis, V. G., Yang, E. S.-H., & Georgakilas, A. G. (2012) · Cancer Letters · doi:10.1016/j.canlet.2012.05.015 · Cited by 36
“Histone modifications include acetylation, methylation, phosphorylation, sumoylation, poly(ADP)-ribosylation, and ubiquitination (Table 1) [10].”
Howe, C. G., Liu, X., Hall, M. N., Slavkovich, V. N., Ilievski, V., Parvez, F., Siddique, A. B., Shahriar, H., Uddin, M. N., Islam, T., et al. (2016) · Environmental Health Perspectives · doi:10.1289/ehp.1510412 · Cited by 35
DNA methylation of amino acid transporter genes in the human placenta
Simner, C., Novakovic, B., Lillycrop, K. A., Bell, C. G., Harvey, N. C., Cooper, C. C., Saffery, R., Lewis, R. M., & Cleal, J. K. (2017) · Placenta · doi:10.1016/j.placenta.2017.10.010 · Cited by 35
Zhai, Y., Li, W., Zhang, Z., Cao, Y., Wang, Z., Zhang, S., & Li, Z. (2017) · Molecular Reproduction and Development · doi:10.1002/mrd.22935 · Cited by 36
Epigenetic changes and their implications in autoimmune hepatitis
Czaja, A. J. (2018) · European Journal of Clinical Investigation · doi:10.1111/eci.12899 · Cited by 36
“• increases transcriptional activity [32] • reduced by methyltransferases [59, 225] • increased by TET enzymes [75–78] Histone modifications”
BackgroundPairwise Proximity‐Differentiated Visualization of Single‐Cell DNA Epigenetic Marks
Xue, J., Chen, F., Su, L., Cao, X., Bai, M., Zhao, Y., Fan, C., & Zhao, Y. (2020) · Angewandte Chemie International Edition · doi:10.1002/anie.202011172 · Cited by 36
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Shin, H. Y., Kwon, M. J., Lee, E. M., Kim, K., Oh, Y. J., Kim, H. S., Hwang, D. H., & Kim, B. G. (2020) · Journal of Neuroscience · doi:10.1523/jneurosci.1745-20.2020 · Cited by 36
“Recent studies reported that DNA methylation status is closely associated with histone modification (Cedar and Bergman, 2009; Rose and Klose, 2014).”
BackgroundEffect of hexavalent chromium on histone biotinylation in human bronchial epithelial cells
Xia, B., Ren, X., Zhuang, Z., Yang, L., Huang, H., Pang, L., Wu, D., Luo, J., Tan, Y.-L., Liu, J., et al. (2014) · Toxicology Letters · doi:10.1016/j.toxlet.2014.05.010 · Cited by 36
Hackett, M. J., Borondics, F., Brown, D. S., Hirschmugl, C. J., Smith, S., Paterson, P. G., Nichol, H., Pickering, I. J., & George, G. N. (2013) · ACS Chemical Neuroscience · doi:10.1021/cn4000346 · Cited by 35
Epigenetic control of tissue-type plasminogen activator synthesis in human endothelial cells
Dunoyer-Geindre, S., & Kruithof, E. K. O. (2011) · Cardiovascular Research · doi:10.1093/cvr/cvr028 · Cited by 37
“These results are in agreement with the concept that methylated CpG dinucleotides at the proximal promoter are associated with gene inactivation (Cedar, Nat Rev Genet 2008).(22)”
Result
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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