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

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DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development

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

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A bivalent chromatin structure marks key developmental genes in embryonic stem cells

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Human DNA methylomes at base resolution show widespread epigenomic differences

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Cancer-associated IDH1 mutations produce 2-hydroxyglutarate

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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

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

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

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The ground state of embryonic stem cell self-renewal

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CpG islands and the regulation of transcription

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DNA methylation: roles in mammalian development

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Oncometabolite 2-Hydroxyglutarate Is a Competitive Inhibitor of α-Ketoglutarate-Dependent Dioxygenases

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A decade of exploring the cancer epigenome—biological and translational implications

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Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

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Leukemic IDH1 and IDH2 Mutations Result in a Hypermethylation Phenotype, Disrupt TET2 Function, and Impair Hematopoietic Differentiation

Figueroa, M. E., Abdel-Wahab, O., Lu, C., Ward, P. S., Patel, J., Shih, A., Li, Y., Bhagwat, N., Vasanthakumar, A., Fernandez, H. F., et al. (2010) · Cancer Cell · doi:10.1016/j.ccr.2010.11.015 · Cited by 2,766 · see citing works

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

Kriaucionis, S., & Heintz, N. (2009) · Science · doi:10.1126/science.1169786 · Cited by 2,700 · see citing works

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification

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Cancer epigenomics: DNA methylomes and histone-modification maps

Esteller, M. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2005 · Cited by 2,150 · see citing works

EUKARYOTIC CYTOSINE METHYLTRANSFERASES

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The Common Feature of Leukemia-Associated IDH1 and IDH2 Mutations Is a Neomorphic Enzyme Activity Converting α-Ketoglutarate to 2-Hydroxyglutarate

Ward, P. S., Patel, J., Wise, D. R., Abdel-Wahab, O., Bennett, B. D., Coller, H. A., Cross, J. R., Fantin, V. R., Hedvat, C. V., Perl, A. E., et al. (2010) · Cancer Cell · doi:10.1016/j.ccr.2010.01.020 · Cited by 2,020 · cited 1× · see citing works

DNA Modification Mechanisms and Gene Activity During Development

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High sensitivity mapping of methylated cytosines

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Global epigenomic reconfiguration during mammalian brain development

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Mutation in <i>TET2</i> in Myeloid Cancers

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Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases

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TET enzymes, TDG and the dynamics of DNA demethylation

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DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA

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UHRF1 Plays a Role in Maintaining DNA Methylation in Mammalian Cells

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DNA-binding factors shape the mouse methylome at distal regulatory regions

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A map of the cis-regulatory sequences in the mouse genome

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Charting a dynamic DNA methylation landscape of the human genome

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Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain

Guo, J. U., Su, Y., Zhong, C., Ming, G., & Song, H. (2011) · Cell · doi:10.1016/j.cell.2011.03.022 · Cited by 1,355 · see citing works

X inactivation, differentiation, and DNA methylation

Riggs, A. D. (2008) · Cytogenetics and Cell Genetics · doi:10.1159/000130315 · Cited by 1,343 · see citing works

Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation

Moran-Crusio, K., Reavie, L., Shih, A., Abdel-Wahab, O., Ndiaye-Lobry, D., Lobry, C., Figueroa, M. E., Vasanthakumar, A., Patel, J., Zhao, X., et al. (2011) · Cancer Cell · doi:10.1016/j.ccr.2011.06.001 · Cited by 1,339 · see citing works

Demethylation of the zygotic paternal genome

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The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA

Sharif, J., Muto, M., Takebayashi, S., Suetake, I., Iwamatsu, A., Endo, T. A., Shinga, J., Mizutani-Koseki, Y., Toyoda, T., Okamura, K., et al. (2007) · Nature · doi:10.1038/nature06397 · Cited by 1,307 · see citing works

Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2

Ko, M., Huang, Y., Jankowska, A. M., Pape, U. J., Tahiliani, M., Bandukwala, H. S., An, J., Lamperti, E. D., Koh, K. P., Ganetzky, R. D., et al. (2010) · Nature · doi:10.1038/nature09586 · Cited by 1,294 · see citing works

JmjC-domain-containing proteins and histone demethylation

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How Are Alkynes Scrambled?

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Epigenetic reprogramming in mouse primordial germ cells

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Inhibition of α-KG-dependent histone and DNA demethylases by fumarate and succinate that are accumulated in mutations of FH and SDH tumor suppressors

Xiao, M., Yang, H., Xu, W., Ma, S., Lin, H., Zhu, H., Liu, L., Liu, Y., Yang, C., Xu, Y., et al. (2012) · Genes &amp; Development · doi:10.1101/gad.191056.112 · Cited by 1,188 · cited 1× · see citing works

Epigenetic Reprogramming in Plant and Animal Development

Feng, S., Jacobsen, S. E., & Reik, W. (2010) · Science · doi:10.1126/science.1190614 · Cited by 1,171 · see citing works

The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes

Gu, T., Guo, F., Yang, H., Wu, H.-P., Xu, G., Liu, W., Xie, Z.-G., Shi, L., He, X., Jin, S., et al. (2011) · Nature · doi:10.1038/nature10443 · Cited by 1,144 · see citing works

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

Ficz, G., Branco, M. R., Seisenberger, S., Santos, F., Krueger, F., Hore, T. A., Marques, C. J., Andrews, S., & Reik, W. (2011) · Nature · doi:10.1038/nature10008 · Cited by 1,123 · see citing works

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine

Song, C., Szulwach, K. E., Fu, Y., Dai, Q., Yi, C., Li, X., Li, Y., Chen, C.-H., Zhang, W., Jian, X., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1732 · Cited by 1,089 · see citing works

Active DNA demethylation: many roads lead to Rome

Wu, S. C., & Zhang, Y. (2010) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2950 · Cited by 1,054 · see citing works

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

Yu, M., Hon, G. C., Szulwach, K. E., Song, C., Zhang, L., Kim, A., Li, X., Dai, Q., Shen, Y., Park, B., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.027 · Cited by 1,022 · see citing works

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

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Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons

Feng, J., Zhou, Y., Campbell, S. L., Le, T., Li, E., Sweatt, J. D., Silva, A. J., & Fan, G. (2010) · Nature Neuroscience · doi:10.1038/nn.2514 · Cited by 1,019 · see citing works

Active demethylation of the paternal genome in the mouse zygote

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The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells

Seisenberger, S., Andrews, S., Krueger, F., Arand, J., Walter, J., Santos, F., Popp, C., Thienpont, B., Dean, W., & Reik, W. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.11.001 · Cited by 973 · see citing works

Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives

Spruijt, C. G., Gnerlich, F., Smits, A. H., Pfaffeneder, T., Jansen, P. W. T. C., Bauer, C., Münzel, M., Wagner, M., Müller, M., Khan, F., et al. (2013) · Cell · doi:10.1016/j.cell.2013.02.004 · Cited by 973 · see citing works

A unique regulatory phase of DNA methylation in the early mammalian embryo

Smith, Z. D., Chan, M. M., Mikkelsen, T. S., Gu, H., Gnirke, A., Regev, A., & Meissner, A. (2012) · Nature · doi:10.1038/nature10960 · Cited by 964 · see citing works

MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system

Mellén, M., Ayata, P., Dewell, S., Kriaucionis, S., & Heintz, N. (2012) · Cell · doi:10.1016/j.cell.2012.11.022 · Cited by 943 · see citing works

Cyclical DNA methylation of a transcriptionally active promoter

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Neuronal Activity–Induced Gadd45b Promotes Epigenetic DNA Demethylation and Adult Neurogenesis

Dengke, K., Jang, M., Guo, J. U., Kitabatake, Y., Chang, M.-L., Pow-anpongkul, N., Flavell, R. A., Lu, B., Ming, G., & Song, H. (2009) · Science · doi:10.1126/science.1166859 · Cited by 929 · see citing works

TET2 Inactivation Results in Pleiotropic Hematopoietic Abnormalities in Mouse and Is a Recurrent Event during Human Lymphomagenesis

Quivoron, C., Couronné, L., Della Valle, V., Lopez, C. K., Plo, I., Wagner-Ballon, O., Do Cruzeiro, M., Delhommeau, F., Arnulf, B., Stern, M.-H., et al. (2011) · Cancer Cell · doi:10.1016/j.ccr.2011.06.003 · Cited by 924 · see citing works

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

Booth, M. J., Branco, M. R., Ficz, G., Oxley, D., Krueger, F., Reik, W., & Balasubramanian, S. (2012) · Science · doi:10.1126/science.1220671 · Cited by 923 · see citing works

Influence of Metabolism on Epigenetics and Disease

Kaelin, W. G., & McKnight, S. L. (2013) · Cell · doi:10.1016/j.cell.2013.03.004 · Cited by 920 · see citing works

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

Pastor, W. A., Aravind, L., & Rao, A. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3589 · Cited by 897 · cited 1× · see citing works

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

Marks, H., Kalkan, T., Menafra, R., Denissov, S., Jones, K. A., Hofemeister, H., Nichols, J., Kranz, A., Stewart, A., Smith, A. G., et al. (2012) · Cell · doi:10.1016/j.cell.2012.03.026 · Cited by 881 · see citing works

Epigenetic events in mammalian germ-cell development: reprogramming and beyond

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Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells

Blaschke, K., Ebata, K. T., Karimi, M. M., Zepeda-Martínez, J. A., Goyal, P., Mahapatra, S., Tam, A., Laird, D. J., Hirst, M., Rao, A., et al. (2013) · Nature · doi:10.1038/nature12362 · Cited by 865 · see citing works

Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates

Globisch, D., Münzel, M., Müller, M., Michalakis, S., Wagner, M., Koch, S., Brückl, T., Biel, M., & Carell, T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015367 · Cited by 865 · see citing works

Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency

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Thymine DNA Glycosylase Can Rapidly Excise 5-Formylcytosine and 5-Carboxylcytosine

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5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging

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Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair

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Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

Pastor, W. A., Pape, U. J., Huang, Y., Henderson, H. R., Lister, R., Ko, M., McLoughlin, E. M., Brudno, Y., Mahapatra, S., Kapranov, P., et al. (2011) · Nature · doi:10.1038/nature10102 · Cited by 804 · see citing works

5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming

Wossidlo, M., Nakamura, T., Lepikhov, K., Marques, C. J., Zakhartchenko, V., Boiani, M., Arand, J., Nakano, T., Reik, W., & Walter, J. (2011) · Nature Communications · doi:10.1038/ncomms1240 · Cited by 793 · see citing works

Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma

Lian, C. G., Xu, Y., Ceol, C., Wu, F., Larson, A., Dresser, K., Xu, W., Tan, L., Hu, Y., Zhan, Q., et al. (2012) · Cell · doi:10.1016/j.cell.2012.07.033 · Cited by 789 · see citing works

Tet1 and Tet2 Regulate 5-Hydroxymethylcytosine Production and Cell Lineage Specification in Mouse Embryonic Stem Cells

Koh, K. P., Yabuuchi, A., Rao, S., Huang, Y., Cunniff, K., Nardone, J., Laiho, A., Tahiliani, M., Sommer, C. A., Mostoslavsky, G., et al. (2011) · Cell Stem Cell · doi:10.1016/j.stem.2011.01.008 · Cited by 776 · see citing works

Germline DNA Demethylation Dynamics and Imprint Erasure through 5-hydroxymethylcytosine

Hackett, J. A., Sengupta, R., Żylicz, J. J., Murakami, K., Lee, C., Down, T., & Surani, M. (2012) · Science · doi:10.1126/science.1229277 · Cited by 762 · see citing works

Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation

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Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2)

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The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

Huang, Y., Pastor, W., Shen, Y.-H., Tahiliani, M., Liu, D. R., & Rao, A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008888 · Cited by 755 · see citing works

Acquired mutations in TET2 are common in myelodysplastic syndromes

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Establishment and maintenance of genomic methylation patterns in mouse embryonic stem cells by Dnmt3a and Dnmt3b

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Active DNA Demethylation Mediated by DNA Glycosylases

Zhu, J. (2009) · Annual Review of Genetics · doi:10.1146/annurev-genet-102108-134205 · Cited by 746 · see citing works

Dynamic CpG island methylation landscape in oocytes and preimplantation embryos

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Pluripotency and Cellular Reprogramming: Facts, Hypotheses, Unresolved Issues

Hanna, J. H., Saha, K., & Jaenisch, R. (2010) · Cell · doi:10.1016/j.cell.2010.10.008 · Cited by 695 · see citing works

Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine

Iqbal, K., Jin, S., Pfeifer, G. P., & Szabó, P. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1014033108 · Cited by 693 · see citing works

Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase

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Reprogramming towards pluripotency requires AID-dependent DNA demethylation

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Deletion of Tet2 in mice leads to dysregulated hematopoietic stem cells and subsequent development of myeloid malignancies

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