Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions

DNA methylation patterns and epigenetic memory

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Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals

Jaenisch, R., & Bird, A. (2003) · Nature Genetics · doi:10.1038/ng1089 · Cited by 6,325

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

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

Tahiliani, M., Koh, K. P., Shen, Y., Pastor, W. A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L. M., Liu, D. R., Aravind, L., et al. (2009) · Science · doi:10.1126/science.1170116 · Cited by 5,836

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

Human DNA methylomes at base resolution show widespread epigenomic differences

Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q.-M., et al. (2009) · Nature · doi:10.1038/nature08514 · Cited by 4,673

Cancer-associated IDH1 mutations produce 2-hydroxyglutarate

Dang, L., White, D. W., Gross, S., Bennett, B. D., Bittinger, M. A., Driggers, E. M., Fantin, V. R., Jang, H. G., Jin, S., Keenan, M. C., et al. (2009) · Nature · doi:10.1038/nature08617 · Cited by 4,154

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

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

Law, J. A., & Jacobsen, S. E. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2719 · Cited by 3,925

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine

Ito, S., Shen, L., Dai, Q., Wu, S. C., Collins, L. B., Swenberg, J. A., He, C., & Zhang, Y. (2011) · Science · doi:10.1126/science.1210597 · Cited by 3,451

Folate: Could We Live Without It? A Novel Epigenetic Connection

Powell, C. A., Villa, G., Holmes, T., & Choudhury, M. (2019) · Springer eBooks · doi:10.1007/978-3-319-55387-0_22 · Cited by 1

Methylation of CpG Sites as Biomarkers Predictive of Drug-Specific Patient Survival in Cancer

Neary, B., Lin, S., & Qiu, P. (2022) · Cancer Informatics · doi:10.1177/11769351221131124 · Cited by 1

A review on Epigenome Editing using CRISPR-based Tools to Rejuvenate Skin Tissues

Sichani, A. S., Baneshi, M., Ranjbar, M., Naeimzadeh, Y., & Fallahi, J. (2023) · International Journal of Bioinformatics and Intelligent Computing · doi:10.61797/ijbic.v2i2.234 · Cited by 1

Integration of RRBS and RNA-seq unravels the regulatory role of DNMT3A in porcine Sertoli cell proliferation

Xu, D., Yan, S., Jin, H., Chen, C., Tang, X., Wang, X., Li, Y., Fei, F., & Yang, A.-Q. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2023.1302351 · Cited by 1

The ageing virus hypothesis: Epigenetic ageing beyond the Tree of Life

Bapteste, E. P. (2024) · BioEssays · doi:10.1002/bies.202400099 · Cited by 2

Advances and insights in cancer metabolism and epigenetic reprogramming

Zeng, Y., Wang, P., & Ye, D. (2025) · Chinese Science Bulletin (Chinese Version) · doi:10.1360/tb-2024-1379 · Cited by 1

Molecular characterization and tissue expression profile of the Dnmts gene family in pig

Luo, Z., Zhang, K., Chen, L., Yuan-xin, Y. A. N. G., Fu, P., Ke-tian, W. A. N. G., Wang, L., Li, M., Li, X., Zuo, F., et al. (2017) · Journal of Integrative Agriculture · doi:10.1016/s2095-3119(16)61512-5 · Cited by 1

Recognition of Oxidized 5‐Methylcytosine Derivatives in DNA by Natural and Engineered Protein Scaffolds

Muñoz‐López, Á., & Summerer, D. (2017) · The Chemical Record · doi:10.1002/tcr.201700088 · Cited by 2

Epigenetic profiling with ultralow DNA amounts

Lin, F., Chien, S., & Chen, Z. (2018) · Nature Biomedical Engineering · doi:10.1038/s41551-018-0211-4 · Cited by 1

TDG regulates cell cycle progression in human neural progenitors

Germanguz, I., Park, J. C., Cinkornpumin, J. K., Solomon, A., Ohashi, M., & Lowry, W. E. (2018) · F1000Research · doi:10.12688/f1000research.13801.1 · Cited by 1

The epigenomic impact of methylation in metabolic dysfunction and cancer

Zahnow, C. A. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-816843-1.00005-9 · Cited by 1

Analysis of 5-Carboxylcytosine Distribution Using DNA Immunoprecipitation

Abakir, A., Alenezi, F., & Ruzov, A. S. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0876-0_24 · Cited by 1

Tet2 regulates Barx2 expression in undifferentiated and early differentiated mouse embryonic stem cells

Qiao, Z., Zhang, S., Hu, T., Lan, F., Yu, D., Ge, G., Li, C., Fang, S.-Q., & Chen, Q. (2020) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2020.09.095 · Cited by 1

Epigenetic Reprogramming by Endocrine Disrupting Chemicals

Chung, F. F., Khoueiry, R., & Herceg, Z. (2020) · Royal Society of Chemistry eBooks · doi:10.1039/9781839160738-00025 · Cited by 1

Coronavirus Disease 19 and Future Ecological Crises: Hopes from Epigenomics and Unraveling Genome Regulation in Humans and Infectious Agents

Dzobo, K. (2021) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2021.0024 · Cited by 1

Epigenetic Bearing on Fertility in Farm Animals

Datta, T. K., Kumar, S., Verma, V., Batra, V., & Kumar, R. (2022) · Springer eBooks · doi:10.1007/978-981-19-0116-4_16 · Cited by 1

Distinct pattern of epigenetic DNA modification in leukocytes from patients with colorectal carcinoma and individuals with precancerous conditions, benign adenoma and inflammatory bowel disease – a link to oxidative stressPreprint

Starczak, M., Zarakowska, E., Modrzejewska, M., Dziaman, T., Szpila, A., Linowiecka, K., Guz, J., Szpotan, J., Gawroński, M., Wołowiec, A., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/141903 · Cited by 1

Epigenetics, the Vascular Wall, and Atherosclerosis

Lund, G., & Zaina, S. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.65409-0 · Cited by 1

Whole human genome 5’-mC methylation analysis using long read nanopore sequencingPreprint

Silva, C., Machado, M. P., Ferrão, J., Rodrigues, A. S., & Vieira, L. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.20.444035 · Cited by 1

Epigenetic regulation of osteoblast differentiation

Najafova, Z. (2017) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-6333 · Cited by 1

AMPK and TET2 Signaling Pathway and their Natural ActivatorsPreprint

Patil, S., Sharma, R., Sharma, U. K., & Padwad, Y. S. (2022) · Preprints.org · doi:10.20944/preprints202204.0100.v1

DNA Methylation is associated with oxidative stress and genomic deregulation in diabetes mellitusPreprint

Sen, S. (2023) · Research Square · doi:10.21203/rs.3.rs-3718690/v1 · Cited by 1

DNA methylation is associated with oxidative stress and genomic deregulation in diabetes mellitusPreprint

Sen, S. (2024) · Research Square · doi:10.21203/rs.3.rs-3718690/v2 · Cited by 1

Metal Coordination and Enzymatic Reaction of the Glioma-Target R132H Isocitrate Dehydrogenase 1: Insights by Molecular SimulationsPreprint

Raghavan, B., Vivo, M. D., & Carloni, P. (2024) · ChemRxiv · doi:10.26434/chemrxiv-2024-jxd73 · Cited by 1

DNA Methylation Signatures of Cardiovascular Health Provide Insights into DiseasesPreprint

Carbonneau, M., Li, Y., Qu, Y., Zheng, Y., Wood, A. C., Wang, M., Liu, C., Huan, T., Joehanes, R., Guo, X., et al. (2024) · medRxiv · doi:10.1101/2024.11.19.24317587 · Cited by 1

DNA Methylation–Based Epigenetic Clocks and Cardiovascular Disease

Li, Y., & Ma, J. (2025) · JACC CardioOncology · doi:10.1016/j.jaccao.2025.07.010 · Cited by 1

Centromeres are hotspots of cytosine methylation epimutations in a filamentous fungusPreprint

de la Peña, M. V., Hull-Crew, C., Hutter, T. R., Vino, C. A., Sarkies, P., Colomé‐Tatché, M., Johannes, F. M., Klocko, A. D., & Kronholm, I. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.03.709258 · Cited by 1

Etude de la pathogénicité pulmonaire des polluants atmosphériques nanoparticulaires

Saleh, Y. (2019) · doi:10.70675/e30143aaz8f0bz4a9azb4fdzc094e6b97e96 · Cited by 1

Predictive Toxicology: Genetics, Genomics, Epigenetics, and Next‐Generation Sequencing in Toxicology

Heckel, T., & Suter‐Dick, L. (2014) · Methods and principles in medicinal chemistry · doi:10.1002/9783527674183.ch08

DNA Methylation: Enzymology

Jurkowska, R. Z., & Jeltsch, A. (2015) · Wiley eBooks · doi:10.1002/9780470015902.a0006156.pub2

Epigenetic alterations in sporadic and familial cancers

Joensuu, E. I. (2015) · Työväentutkimus Vuosikirja

Epigenetic Dysregulation in Cutaneous Malignant Melanoma: Advancing Approaches to Diagnosis, Prognosis, and Therapeutic Targeting

Lee, J. J. (2015) · Digital Access to Scholarship at Harvard (DASH) (Harvard University)

Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite

Wu, H., Wu, X., Shen, L., & Zhang, Y. (2014)

The role of thymine DNA glycosylase (TDG) and DNA demethylation in TGF beta signaling

Maitland, M. E. R. (2015) · Scholarship@Western (Western University)

Identification of common and distinct epigenetic re-programming properties of Core-Binding Factor (CBF) Fusion Proteins

Loke, J. C. T., Ptasinska, A., Imperato, M. R., Assi, S. A., Cauchy, P., Cowell, I. G., Heidenreich, O. T., Raghavan, M., Delwel, R., Cockerill, P., et al. (2016) · Klinische Pädiatrie · doi:10.1055/s-0036-1582520

'Memory and molecular turnover,' 30 years after

Meagher, R. B. (2014)

Lipids and Epigenetics

Burdge, G. C. (2016) · WORLD SCIENTIFIC eBooks · doi:10.1142/9789813143319_0004

Epigenetics in Development, Differentiation and Reprogramming

Salts, N., & Meshorer, E. (2016) · Springer eBooks · doi:10.1007/978-3-319-38882-3_18

Aberrant Patterns of DNA Methylation in Cancer

Hudler, P. (2016) · Wiley eBooks · doi:10.1002/9780470015902.a0006160

Base Excision Repair and Epigenetic Regulation

Weber, A. R., & Schuermann, D. (2016) · WORLD SCIENTIFIC eBooks · doi:10.1142/9789814719735_0011

The aging immune system and nutritional interventions

van Beek, A. A. (2017) · doi:10.18174/392235

Investigação da variação da metilação de DNA em macrófagos de camundongos infectados com L.(L.)amazonensis e L.(L.)infantum

Marçola, T. G. (2016) · doi:10.26512/2016.02.t.22189

Frequency of L1721W Polymorphism in TET2 Gene Among a Cohort of Sudanese Patients with Myeloproliferative Disorders: Possible Roles in Pathogenicity and Leukemic Transformation

Ibrahim, A. A. (2017) · International Journal of Genetics and Genomics · doi:10.11648/j.ijgg.20170505.11

Epigenetic reprogramming and DNA demethylation

Bagci, H. (2014) · Spiral (Imperial College London) · doi:10.25560/45352

DNA/Histone Methylation and Adipocyte Differentiation: Applications to Obesity

Yuan, Y., Liu, C., Wan, D., Huang, K., & Zheng, L. (2019) · Springer eBooks · doi:10.1007/978-3-319-55530-0_96

Folate: Could We Live Without It? A Novel Epigenetic Connection

Powell, C. A., Villa, G., Holmes, T., & Choudhury, M. (2017) · Springer eBooks · doi:10.1007/978-3-319-40007-5_22-1

The role of epigenetical modifications in tuberculosis

Zhu, C., Zhang, Z., & XinChun, C. H. E. N. (2017) · Scientia Sinica Vitae · doi:10.1360/n052017-00226

No Oxygen? No Problem! Epigenetic mechanisms of anoxia tolerance in a champion anaerobe, the red-eared slider turtle (Trachemys scripta elegans)

Wijenayake, S. (2017) · Carleton University's Institutional Repository (MacOdrum Library, Carleton University) · doi:10.22215/etd/2017-12053

Designing Epigenome Editing Tools to Understand the Functional Role of DNA Methylation Changes in Cancer

McDonald, J. I. (2017) · Open Scholarship Institutional Repository (Washington University in St. Louis) · doi:10.7936/k73f4p2b

Neuronal Growth Factor regulates Brain Specific Kinase 1 expression by inhibiting promoter methylation and promoting Sp1 recruitment

Martínez, L. R., Vargas, M. A., Espadamala, J., Gómez, N., Lizcano, J. M., & López‐Bayghen, E. (2018) · Neurochemistry International · doi:10.1016/j.neuint.2018.08.014

Pain-Induced Chromatin Modifications

Pan, Z. Z., Zhou, C., Wu, Y., Zhang, Z., & Cai, Y. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-814070-3.00006-5

WDR76 Promotes MLL-Rearranged Leukemia Via Selective Recognition of 5-Hydroxymethylcytosine in DNAPreprint

Malecek, K. E., Weng, H., Sullivan, M. A., Kokontis, C., Werner, M. S., Chen, J., & Ruthenburg, A. J. (2019) · SSRN Electronic Journal · doi:10.1101/511394

Cell-type-specific epigenetics of organ-derived neurons and adipocytes

Yu, P. (2017)

Mechanizmy kontrolujące strukturę chromatyny

Sacharowski, S., & Sarnowski, T. J. (2019) · Postępy Biochemii · doi:10.18388/pb.2019_252

Coordination of Replication-Coupled Protein Destruction and Origin Licensing Control During Cell Cycle Transitions

Coleman, K. E. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/nhap-ah54

role of brain iron loading in redox-epigenetic regulation of psychiatrics-like behavior

Ye, X. (2018) · Digital Repository Service (Northeastern University) · doi:10.17760/d20285816

Base-Resolution and Single-Cell Analysis of Active DNA Demethylation Using Methylase-Assisted Bisulfite Sequencing

Wu, X. (2018) · Digital Access to Scholarship at Harvard (DASH) (Harvard University)

Dynamic regulation of DNA methylation in human T-cell biology

Lentini, A. (2019) · Linköping University medical dissertations · doi:10.3384/diss.diva-155116

Epigenetic regulation by BAF (mSWI/SNF) chromatin remodeling complexes in late cortical development and beyond

Nguyen, H. (2019) · doi:10.53846/goediss-7621

Modelling Folate Metabolism and DNA Methylation

Auley, M. T. M. (2019) · Springer eBooks · doi:10.1007/978-3-319-39994-2_8

Genome-wide DNA methylation and imprinted gene analysis in babies conceived by ART

Gooding, L. D. (2019) · cIRcle (University of British Columbia) · doi:10.14288/1.0384565

Genetic influences on PTSD

Bountress, K. E., Brick, L. A. D., Cusack, S. E., Sheerin, C. M., Nugent, N. R., & Amstadter, A. B. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-816022-0.00008-9

Cortical patterning and neuronal migration are under the guide of BAF complex functionality

Sokpor, G. (2020) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-7927

Genes and cancer: Implications for FHH analysis

Henrich, V. C., Orlando, L. A., & Shirts, B. H. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-816015-2.00005-5

Bisulfite PCR of repetitive genomic sequences

Dunaeva, M. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-819414-0.00006-9

PROGRAMA DE INTERVENÇÃO RECONSTRUINDO AS EMOÇÕES NA PARENTALIDADE

Carvalho, D. M. D. L. (2024) · polemica · doi:10.12957/polemica.2022.84830

Distinct epigenetic regulation in patients with multidrug-resistant TB-HIV co-infection and uninfected individuals

Marimani, M. D., Alomar, S. Y., Aldahmash, B. A., Ahmad, A., Stacey, S. L., & Duse, A. G. (2020) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2020.111724

Verification and analysis of methylation profile assay data from RA CD4+ T cells by Bisulphite Sequencing

Rogers, J. H. (2018) · White Rose eTheses Online (University of Leeds, The University of Sheffield, University of York)

Epigenetics in cardiac development and human induced pluripotent stem cells

Majo, F. D., Kuster, G. M., & Windt, L. J. D. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-822258-4.00017-1

The role of TET1 and TET1ALT in cancer

Good, C. R. (2017) · TUScholarShare (Temple University)

Biological Background—Information, Energy, and Matter

Lei, J. (2021) · Lecture notes on mathematical modelling in the life sciences · doi:10.1007/978-3-030-73033-8_1

Quantitative Assessment of the Oxidation Products of 5-Methylcytosine in DNA by Liquid Chromatography-Tandem Mass Spectrometry

Yin, J., Liu, S., & Wang, Y. (2021) · Springer protocols handbooks/Springer protocols · doi:10.1007/978-1-0716-1229-3_1

Overview on Epigenetics and Cancer

Youness, E. R. (2020) · Clinical Medical Reviews and Reports · doi:10.31579/2690-8794/015

The Short Isoform TET1s Retards Oscillatory Shear Flow-Induced Atherosclerosis Through CX40-Dependent Endothelial Cell Barrier EnhancementPreprint

Qu, K., Wang, C., Huang, L., Qin, X., Zhang, K., Zhong, Y., Ma, Q., Yan, W., Li, T., Peng, Q., et al. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3944598

Mechanism of DNA Methylation in Stem Cells

Cai, Y., Dong, Q., & Li, A. (2022) · Lecture notes on data engineering and communications technologies · doi:10.1007/978-3-030-89698-0_96

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Direct Read and Quantify Damage Nucleotide from an Oligonucleotide Using a Single Molecule InterfacePreprint

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Epigenetics

Filipowicz, A. R., Chen, Q., & Allard, P. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-95488-4.00139-x

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The Molecular Basis of DNA Demethylation

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