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

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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Histone H3K27ac separates active from poised enhancers and predicts developmental state

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

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

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

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Polycomb complexes repress developmental regulators in murine embryonic stem cells

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Genome-scale DNA methylation maps of pluripotent and differentiated cells

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Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells

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Combined methylation mapping of 5mC and 5hmC during early embryonic stages in bovine

de Montera, B., Fournier, É., Saadi, H. A. S., Gagné, D., Laflamme, I., Blondin, P., Sirard, M., & Robert, C. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-406 · Cited by 18

Epigenetics of Schizophrenia

Gavin, D. P., & Floreani, C. V. (2014) · International review of neurobiology · doi:10.1016/b978-0-12-801311-3.00005-6 · Cited by 17

A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways

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Coprinopsis cinerea

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A Lexicon of DNA Modifications: Their Roles in Embryo Development and the Germline

Zhu, Q., Stöger, R. J., & Alberio, R. (2018) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2018.00024 · Cited by 21

Deciphering Epigenetic Cytosine Modifications by Direct Molecular Recognition

Kubik, G., & Summerer, D. (2015) · ACS Chemical Biology · doi:10.1021/acschembio.5b00158 · Cited by 17

Perturbing TET2 condensation promotes aberrant genome-wide DNA methylation and curtails leukaemia cell growth

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JBP1-seq: A fast and efficient method for genome-wide profiling of 5hmC

Cui, L., Chung, T. H., Tan, D., Sun, X., & Jia, X.-Y. (2014) · Genomics · doi:10.1016/j.ygeno.2014.08.023 · Cited by 17

A guide to stem cell identification: Progress and challenges in system‐wide predictive testing with complex biomarkers

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5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation

Kranzhöfer, D., Gilsbach, R., Grüning, B. A., Backofen, R., Nührenberg, T. G., & Hein, L. (2016) · PLoS ONE · doi:10.1371/journal.pone.0166575 · Cited by 17

Chemistry‐Driven Epigenetic Investigation of Histone and DNA Modifications

Sueoka, T., Koyama, K., Hayashi, G., & Okamoto, A. (2018) · The Chemical Record · doi:10.1002/tcr.201800040 · Cited by 17

Deciphering the multifaceted roles of TET proteins in T‐cell lineage specification and malignant transformation

Tsagaratou, A. (2021) · Immunological Reviews · doi:10.1111/imr.12940 · Cited by 16

Measurements of DNA Methylation at Seven Loci in Various Tissues of CD1 Mice

Daugela, L., Nüsgen, N., Walier, M., Oldenburg, J., Schwaab, R., & El‐Maarri, O. (2012) · PLoS ONE · doi:10.1371/journal.pone.0044585 · Cited by 17

Changes in the DNA Methylation and Hydroxymethylation Status of the Intercellular Adhesion Molecule 1 Gene Promoter in Thyrocytes from Autoimmune Thyroiditis Patients

Liu, T., Sun, J., Wang, Z., Yang, W., Zhang, H., Fan, C., Shan, Z., & Teng, W. (2017) · Thyroid · doi:10.1089/thy.2016.0576 · Cited by 17

Crosstalk Between DNA and Histones: Tet’s New Role in Embryonic Stem Cells

Sui, X., Price, C. O., Li, Z., & Chen, J. (2012) · Current Genomics · doi:10.2174/138920212803759730 · Cited by 17

5‐Formylcytosin ist vermutlich eine semipermanente Base an definierten Genompositionen

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Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns

Tost, J. (2022) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-11454-0_16 · Cited by 15

A Novel method for the simultaneous identification of methylcytosine and hydroxymethylcytosine at a single base resolution

Kawasaki, Y., Kuroda, Y., Suetake, I., Tajima, S., Ishino, F., & Kohda, T. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw994 · Cited by 16

Quantitation and mapping of the epigenetic marker 5‐hydroxymethylcytosine

Qing, Y., Tian, Z., Bi, Y., Wang, Y., Long, J., Song, C., & Diao, J. (2017) · BioEssays · doi:10.1002/bies.201700010 · Cited by 16

5-Hydroxymethylcytosine: a key epigenetic mark in cancer and chemotherapy response

Kharat, S. S., & Sharan, S. K. (2025) · Epigenetics & Chromatin · doi:10.1186/s13072-025-00636-z · Cited by 16

Prenatal lead (Pb) exposure is associated with differential placental DNA methylation and hydroxymethylation in a human population

Tung, P. W., Kennedy, E. M., Burt, A., Hermetz, K. E., Karagas, M. R., & Marsit, C. J. (2022) · Epigenetics · doi:10.1080/15592294.2022.2126087 · Cited by 15

High-throughput single nucleotide variant discovery in E14 mouse embryonic stem cells provides a new reference genome assembly

Incarnato, D., Křepelová, A., & Neri, F. (2014) · Genomics · doi:10.1016/j.ygeno.2014.06.007 · Cited by 15

The dynamic changes of DNA methylation in primordial germ cell differentiation

Duan, L., Liu, Y., Wang, J., Liao, J., & Hu, J. (2016) · Gene · doi:10.1016/j.gene.2016.06.036 · Cited by 14

Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue

Wilkins, O. M., Johnson, K. C., Houseman, E. A., King, J. E., Marsit, C. J., & Christensen, B. C. (2019) · Epigenetics · doi:10.1080/15592294.2019.1695332 · Cited by 16

Late-occurring chromosome aberrations and global DNA methylation in hematopoietic stem/progenitor cells of CBA/CaJ mice exposed to silicon (28Si) ions

Rithidech, K. N., Honikel, L., Reungpatthanaphong, P., Tungjai, M., Jangiam, W., & Whorton, E. B. (2015) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2015.09.001 · Cited by 14

Recent advance in optical single-molecule detection of methylation modification and methyl-modifying enzymes

Han, Y., Yang, D., Jiang, S., Zhao, S., Ma, F., & Zhang, C. (2024) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2024.117553 · Cited by 14

Advances in Understanding the Coupling of DNA Base Modifying Enzymes to Processes Involving Base Excision Repair

Wyatt, M. D. (2013) · Advances in cancer research · doi:10.1016/b978-0-12-407190-2.00002-2 · Cited by 14

Inhibition ofMspI cleavage activity by hydroxymethylation of the CpG site: A concern for DNA modification studies using restriction endonucleases

Ichiyanagi, K. (2012) · Epigenetics · doi:10.4161/epi.7.2.18909 · Cited by 14

Perturbations of 5-Hydroxymethylcytosine Patterning in Hematologic Malignancies

Madžo, J., Vasanthakumar, A., & Godley, L. A. (2013) · Seminars in Hematology · doi:10.1053/j.seminhematol.2013.01.004 · Cited by 14

Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion identifies evolutionarily unconserved CpGs as TET targets

Sérandour, A. A., Avner, S., Mahé, E. A., Madigou, T., Guibert, S., Weber, M., & Salbert, G. (2016) · Genome biology · doi:10.1186/s13059-016-0919-y · Cited by 14

Asymmetric DNA methylation of CpG dyads is a feature of secondary DMRs associated with the Dlk1/Gtl2 imprinting cluster in mouse

Guntrum, M., Vlasova, E., & Davis, T. L. (2017) · Epigenetics & Chromatin · doi:10.1186/s13072-017-0138-0 · Cited by 15

The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function

Battistini, F., Dans, P. D., Terrazas, M., Castellazzi, C. L., Portella, G., Labrador, M., Villegas, N., Heath, I. B., González, C., & Orozco, M. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009547 · Cited by 16

Single‐Molecule Detection of 5‐Hydroxymethylcytosine in DNA through Chemical Modification and Nanopore Analysis

Li, W., Gong, L., & Bayley, H. (2013) · Angewandte Chemie · doi:10.1002/ange.201300413 · Cited by 14

Dual functions of TET1 in germ layer lineage bifurcation distinguished by genomic context and dependence on 5-methylcytosine oxidation

van der Veer, B. K., Chen, L., Custers, C., Athanasouli, P., Schroiff, M., Cornelis, R., Chui, J. S., Finnell, R. H., Lluís, F., & Koh, K. P. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad231 · Cited by 17

Mind-Body Interrelationship in DNA Methylation

Szyf, M. (2012) · Chemical immunology/Fortschritte der Allergielehre/Progress in allergy/Chemical immunology and allergy · doi:10.1159/000336503 · Cited by 14

Genome-wide 5-hydroxymethylcytosine modification pattern is a novel epigenetic feature of globozoospermia

Wang, X.-X., Sun, B.-F., Jiao, J., Chong, Z.-C., Chen, Y.-S., Wang, X.-L., Zhao, Y., Zhou, Y.-M., & Li, D. (2015) · Oncotarget · doi:10.18632/oncotarget.3163 · Cited by 14

Meeting the methodological challenges in molecular mapping of the embryonic epigenome

McGraw, S., Saadi, H. A. S., & Robert, C. (2013) · Molecular Human Reproduction · doi:10.1093/molehr/gat046 · Cited by 14

Single-base resolution analysis of DNA epigenome via high-throughput sequencing

Peng, J., Xia, B., & Yi, C. (2016) · Science China Life Sciences · doi:10.1007/s11427-016-5013-x · Cited by 14

Simple and cost-effective fluorescent labeling of 5-hydroxymethylcytosine

Shahal, T., Green, O., Hananel, U., Michaeli, Y., Shabat, D., & Ebenstein, Y. (2016) · Methods and Applications in Fluorescence · doi:10.1088/2050-6120/4/4/044003 · Cited by 14

Nichtkanonische Basen im Genom: die regulative Informationsebene in der DNA

Carell, T., Kurz, M. Q., Müller, M., Rossa, M., & Spada, F. (2017) · Angewandte Chemie · doi:10.1002/ange.201708228 · Cited by 14

Chemo‐Enzymatic Fluorescence Labeling Of Genomic DNA For Simultaneous Detection Of Global 5‐Methylcytosine And 5‐Hydroxymethylcytosine**

Avraham, S., Schütz, L., Käver, L., Dankers, A., Margalit, S., Michaeli, Y., Zirkin, S., Torchinsky, D., Gilat, N., Bahr, O., et al. (2023) · ChemBioChem · doi:10.1002/cbic.202300400 · Cited by 13

5-Hydroxymethylcytosine Profiling of Cell-Free DNA Identifies Bivalent Genes That Are Prognostic of Survival in High-Risk Neuroblastoma

Chennakesavalu, M., Moore, K., Chaves, G. S., Veeravalli, S., TerHaar, R., Wu, T., Lyu, R., Chlenski, A., He, C., Piunti, A., et al. (2024) · JCO Precision Oncology · doi:10.1200/po.23.00297 · Cited by 15

Integrative Analysis of the Acquisition of Pluripotency in PGCs Reveals the Mutually Exclusive Roles of Blimp-1 and AKT Signaling

Nagamatsu, G., Saito, S., Takubo, K., & Suda, T. (2015) · Stem Cell Reports · doi:10.1016/j.stemcr.2015.05.007 · Cited by 13

Polymerization retardation isothermal amplification (PRIA): a strategy enables sensitively quantify genome-wide 5-methylcytosine oxides rapidly on handy instruments with nanoscale sample input

Chen, D., Wang, Y., Mo, M., Zhang, J., Zhang, Y., Xu, Y., Liu, S. M., Chen, J., Ma, Y., Zhang, L., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz704 · Cited by 13

SyStemCell: A Database Populated with Multiple Levels of Experimental Data from Stem Cell Differentiation Research

Yu, J., Xing, X., Zeng, L., Sun, J., Li, W., Sun, H., He, Y., Li, J., Zhang, G., Wang, C., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035230 · Cited by 13

Subsets of Visceral Adipose Tissue Nuclei with Distinct Levels of 5-Hydroxymethylcytosine

Yu, P., Ji, L., Lee, K. J., Yu, M., He, C., Ambati, S., McKinney, E. C., Jackson, C. L., Baile, C. A., Schmitz, R. J., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0154949 · Cited by 13

Complete, Programmable Decoding of Oxidized 5-Methylcytosine Nucleobases in DNA by Chemoselective Blockage of Universal Transcription-Activator-Like Effector Repeats

Gieß, M., Witte, A., Jasper, J., Koch, O., & Summerer, D. (2018) · Journal of the American Chemical Society · doi:10.1021/jacs.8b02909 · Cited by 13

Structural basis for the substrate selectivity of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease

Shao, C., Wang, C., & Zang, J. (2014) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s139900471401606x · Cited by 13

Peroxotungstate oxidation-mediated two-phase amplification system (POM-TPAS) for bisulfite-free quantification of locus-specific 5-hydroxymethylcytosine

Zhang, Z., Yan, J., & Li, Z. (2020) · Chemical Communications · doi:10.1039/d0cc00167h · Cited by 12

Epigenetic Regulation of Corneal Epithelial Differentiation by TET2

Sasamoto, Y., Wu, S., Lee, C. A. A., Jiang, J., Ksander, B. R., Frank, M. H., & Frank, N. Y. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24032841 · Cited by 12

Genome-wide profiling of DNA 5-hydroxymethylcytosine during rat Sertoli cell maturation

Landfors, M., Johansen, J. A., Aronsen, J. M., Vågbø, C. B., Doré, L. C., He, C., Sjaastad, I., Sætrom, P., Fedorcsák, P., Dahl, J. A., et al. (2017) · Cell Discovery · doi:10.1038/celldisc.2017.13 · Cited by 12

The dynamics of DNA methylation and hydroxymethylation during amelogenesis

Yoshioka, H., Minamizaki, T., & Yoshiko, Y. (2015) · Histochemistry and Cell Biology · doi:10.1007/s00418-015-1353-z · Cited by 12

The Use of Reverse Phase Protein Arrays (RPPA) to Explore Protein Expression Variation within Individual Renal Cell Cancers

O’Mahony, F. C., Nanda, J., Laird, A., Mullen, P., Caldwell, H., Overton, I. M., Eöry, L., O’Donnell, M., Faratian, D., Powles, T. B., et al. (2013) · Journal of Visualized Experiments · doi:10.3791/50221 · Cited by 11

Eyes on DNA methylation: current evidence for DNA methylation in ocular development and disease

Otteson, D. C. (2011) · Journal of ocular biology, diseases, and informatics · doi:10.1007/s12177-012-9078-x · Cited by 12

Immunohistochemical Detection of 5-Methylcytosine and 5-Hydroxymethylcytosine in Developing and Postmitotic Mouse Retina

Singh, R. K., Diaz, P. E., Binette, F., & Nasonkin, I. O. (2018) · Journal of Visualized Experiments · doi:10.3791/58274 · Cited by 12

Mutations in epigenetic modifiers in acute myeloid leukemia and their clinical utility

Hou, H., & Tien, H. (2016) · Expert Review of Hematology · doi:10.1586/17474086.2016.1144469 · Cited by 13

Concomitant loss of TET2 and TET3 results in T cell expansion and genomic instability in mice

Gioulbasani, M., Äijö, T., Liu, S., Montgomery, S. A., Montgomery, N. D., Corcoran, D. L., & Tsagaratou, A. (2024) · Communications Biology · doi:10.1038/s42003-024-07312-0 · Cited by 12

Loss of 5-hydroxymethylcytosine as a Poor Prognostic Factor for Primary Testicular Diffuse Large B-cell Lymphoma

Shen, Y., Wang, L., Ou, J.-P., Wang, B., & Cen, X. (2022) · International Journal of Medical Sciences · doi:10.7150/ijms.65517 · Cited by 11

Current methods of extracellular DNA methylation analysis

Bryzgunova, O. E., & Laktionov, P. P. (2017) · Molecular Biology · doi:10.1134/s0026893317010071 · Cited by 11

Sulfinate Based Selective Labeling of 5-Hydroxymethylcytosine: Application to Biotin Pull Down Assay

Wu, Q., Amrutkar, S. M., & Shao, F. (2018) · Bioconjugate Chemistry · doi:10.1021/acs.bioconjchem.7b00826 · Cited by 11

TET mediated epigenetic regulation of iNKT cell lineage fate choice and function

Tsagaratou, A. (2018) · Molecular Immunology · doi:10.1016/j.molimm.2018.08.020 · Cited by 10

Improving waste activated sludge dewaterability with sodium periodate pre‐oxidation on extracellular polymeric substances

Lan, B., Jin, R., Liu, G., Dong, B., Zhou, J., & Xing, D. (2021) · Water Environment Research · doi:10.1002/wer.1553 · Cited by 11

The chromatin remodelling protein LSH/HELLS regulates the amount and distribution of DNA hydroxymethylation in the genome

de Dieuleveult, M., Bizet, M., Colin, L., Calonne, E., Bachman, M., Li, C., Stancheva, I., Miotto, B., Fuks, F., & Deplus, R. (2021) · Epigenetics · doi:10.1080/15592294.2021.1917152 · Cited by 13

New functions for DNA modifications by TET-JBP

Huang, Y., & Rao, A. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2437 · Cited by 11

Epigenetic Reprogramming in Cancer

Lindroth, A. M., Park, Y. J., & Plass, C. (2014) · Epigenetics and human health · doi:10.1007/978-3-642-31974-7_9 · Cited by 12

5-Hydroxymethylcytosine signals in serum are a predictor of chemoresistance in high-grade serous ovarian cancer

Weigert, M., Cui, X., West-Szymanski, D. C., Yu, X., Bilecz, A. J., Zhang, Z., Dhir, R., KEHOE, M. J., Zhang, W., He, C., et al. (2024) · Gynecologic Oncology · doi:10.1016/j.ygyno.2024.01.001 · Cited by 10

Cell-Free DNA Hydroxymethylation in Cancer: Current and Emerging Detection Methods and Clinical Applications

Li, J. J. N., Liu, G., & Lok, B. H. (2024) · Genes · doi:10.3390/genes15091160 · Cited by 11

Fundamentals of DNA methylation in development

Gillespie, C. A., Chowdhury, A., Quinn, K. A., Jenkins, M. W., Rollins, A. M., Watanabe, M., & Ford, S. M. (2024) · Pediatric Research · doi:10.1038/s41390-024-03674-7 · Cited by 15

Transformer-based deep learning for accurate detection of multiple base modifications using single molecule real-time sequencing

Hu, X., Shi, Y., Cheng, S. H., Huang, Z., Zhou, Z. G., Shi, X., Zhang, Y., Liu, J., Ma, M.-J. L., Ding, S. C., et al. (2025) · Communications Biology · doi:10.1038/s42003-025-08009-8 · Cited by 11

Overcoming conservation in TALE–DNA interactions: a minimal repeat scaffold enables selective recognition of an oxidized 5-methylcytosine

Maurer, S., Buchmuller, B. C., Ehrt, C., Jasper, J., Koch, O., & Summerer, D. (2018) · Chemical Science · doi:10.1039/c8sc01958d · Cited by 10

The Role of Nucleosomes in Epigenetic Gene Regulation

Giles, K. A., & Taberlay, P. C. (2019) · Springer eBooks · doi:10.1007/978-981-13-8958-0_4 · Cited by 10

Co-Localization of DNA i-Motif-Forming Sequences and 5-Hydroxymethyl-cytosines in Human Embryonic Stem Cells

Bhavsar-Jog, Y. P., Dornshuld, E. V., Brooks, T. A., Tschumper, G. S., & Wadkins, R. M. (2019) · Molecules · doi:10.3390/molecules24193619 · Cited by 10

The Epigenetic Landscape of Aneuploidy: Constitutional Mosaicism Leading the Way?

Davidsson, J. (2014) · Epigenomics · doi:10.2217/epi.13.78 · Cited by 11

Epigenetic regulation in the neurogenic niche of the adult dentate gyrus

Sheehy, R. N., Quintanilla, L., & Song, J. (2021) · Neuroscience Letters · doi:10.1016/j.neulet.2021.136343 · Cited by 10

Chemical Biology Approaches to Identify and Profile Interactors of Chromatin Modifications

Nickel, G. A., & Diehl, K. L. (2022) · ACS Chemical Biology · doi:10.1021/acschembio.1c00794 · Cited by 9

Practical Guidelines and Consideration of Using RRHP for 5hmC Detection

Sun, X., Chung, T. H., Tan, D., & Kim, A. (2016) · Epigenomics · doi:10.2217/epi.15.105 · Cited by 9

High-throughput sequencing offers new insights into 5-hydroxymethylcytosine

Pang, A. P. S., Sugai, C. K., & Maunakea, A. K. (2016) · BioMolecular Concepts · doi:10.1515/bmc-2016-0011 · Cited by 9

High-Throughput Sequencing-Based Mapping of Cytosine Modifications

Bernstein, A. I., & Jin, P. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-801080-8.00003-x · Cited by 9

Preferential 5‐Methylcytosine Oxidation in the Linker Region of Reconstituted Positioned Nucleosomes by Tet1 Protein

Kizaki, S., Zou, T., Li, Y., Han, Y.-W., Suzuki, Y., Harada, Y., & Sugiyama, H. (2016) · Chemistry - A European Journal · doi:10.1002/chem.201602435 · Cited by 9

Compilation of Modern Technologies To Map Genome‐Wide Cytosine Modifications in DNA

Zeng, H., He, B., & Yi, C. (2019) · ChemBioChem · doi:10.1002/cbic.201900035 · Cited by 9

Effects of Dimethyl Sulfoxide on the Pluripotency and Differentiation Capacity of Mouse Embryonic Stem Cells

Yi, J., Park, S., Ha, J. J., Kim, D., Huang, H., Park, S., Lee, M., Ryoo, Z. Y., Kim, S., & Kim, M.-O. (2020) · Cellular Reprogramming · doi:10.1089/cell.2020.0006 · Cited by 9

Nonenzymatic Labeling of 5‐Hydroxymethylcytosine in Nanopore Sequencing

Lu, X., & He, C. (2013) · ChemBioChem · doi:10.1002/cbic.201300342 · Cited by 9

The Contribution of Next Generation Sequencing Technologies to Epigenome Research of Stem Cell and Tumorigenesis

Li, J. (2013) · Human Genetics & Embryology · doi:10.4172/2161-0436.s2-001 · Cited by 8

DNA Labeling Using DNA Methyltransferases

Tomkuvienė, M., Kriukienė, E., & Klimašauskas, S. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-43624-1_19 · Cited by 9

Cytosine 5-hydroxymethylation regulates VHL gene expression in renal clear cell carcinoma

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Guanine quadruplexes and their roles in molecular processes

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