The DOI matches its Crossref record; 28 of the 28 references it cites were found in a registry or an index.
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
Open accessAbstract
5-hydroxymethylcytosine (5hmC) is a modified base present at low levels in diverse cell types in mammals. 5hmC is generated by the TET family of Fe(II) and 2-oxoglutarate-dependent enzymes through oxidation of 5-methylcytosine (5mC). 5hmC and TET proteins have been implicated in stem cell biology and cancer, but information on the genome-wide distribution of 5hmC is limited. Here we describe two novel and specific approaches to profile the genomic localization of 5hmC. The first approach, termed GLIB (glucosylation, periodate oxidation, biotinylation) uses a combination of enzymatic and chemical steps to isolate DNA fragments containing as few as a single 5hmC. The second approach involves conversion of 5hmC to cytosine 5-methylenesulphonate (CMS) by treatment of genomic DNA with sodium bisulphite, followed by immunoprecipitation of CMS-containing DNA with a specific antiserum to CMS. High-throughput sequencing of 5hmC-containing DNA from mouse embryonic stem (ES) cells showed strong enrichment within exons and near transcriptional start sites. 5hmC was especially enriched at the start sites of genes whose promoters bear dual histone 3 lysine 27 trimethylation (H3K27me3) and histone 3 lysine 4 trimethylation (H3K4me3) marks. Our results indicate that 5hmC has a probable role in transcriptional regulation, and suggest a model in which 5hmC contributes to the 'poised' chromatin signature found at developmentally-regulated genes in ES cells.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Genome-wide enrichment studies in human and mouse embryonic stem cells (ESCs) confirms the presence of 5hmC at promoters and enhancers in addition to gene bodies (20).”
From Hepatocyte Nuclear Factor 4‐Alpha Is Essential for the Active Epigenetic State at Enhancers in Mouse Liver (2019) · cites this paper as [20]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
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
Self-citationA 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
Self-citationHistone H3K27ac separates active from poised enhancers and predicts developmental state
Creyghton, M. P., Cheng, A. W., Welstead, G. G., Kooistra, T., Carey, B. W., Steine, E. J., Hanna, J., Lodato, M. A., Frampton, G. M., Sharp, P. A., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016071107 · Cited by 4,302
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
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
Ito, S., D’Alessio, A. C., Taranova, O., Hong, K., Sowers, L. C., & Zhang, Y. (2010) · Nature · doi:10.1038/nature09303 · Cited by 2,628
Polycomb complexes repress developmental regulators in murine embryonic stem cells
Boyer, L. A., Plath, K., Zeitlinger, J., Brambrink, T., Medeiros, L. A., Lee, T. I., Levine, S. S., Wernig, M., Tajonar, A., Ray, M. K., et al. (2006) · Nature · doi:10.1038/nature04733 · Cited by 2,568
Genome-scale DNA methylation maps of pluripotent and differentiated cells
Meissner, A., Mikkelsen, T. S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B. E., Nusbaum, C., Jaffe, D. B., et al. (2008) · Nature · doi:10.1038/nature07107 · Cited by 2,536
Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells
Lee, T. I., Jenner, R. G., Boyer, L. A., Guenther, M. G., Levine, S. S., Kumar, R., Chevalier, B. S., Johnstone, S. E., Cole, M. F., Isono, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.043 · Cited by 2,296
Flagged first, then by citations
Cited by
Sorted by citations
Items 301–400 of 814
Ye, C., & Li, L. (2013) · Cancer Biology & Therapy · doi:10.4161/cbt.27144 · Cited by 56
The Genetic and Epigenetic Journey of Embryonic Stem Cells into Mature Neural Cells
Olynik, B. M., & Rastegar, M. (2012) · Frontiers in Genetics · doi:10.3389/fgene.2012.00081 · Cited by 58
Zhang, L., Chen, W., Iyer, L. M., Hu, J. F., Wang, G., Fu, Y., Yu, M., Dai, Q., Aravind, L., & He, C. (2014) · Journal of the American Chemical Society · doi:10.1021/ja500979k · Cited by 55
Cui, L., Hu, J., Wang, M., Li, C.-C., & Zhang, C. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b04663 · Cited by 53
Horemans, N., Spurgeon, D. J., Lecomte-Pradines, C., Saenen, E., Bradshaw, C., Oughton, D. H., Rasnaca, I., Kamstra, J. H., & Adam‐Guillermin, C. (2019) · Environmental Pollution · doi:10.1016/j.envpol.2019.04.125 · Cited by 59
Zhao, X., Dai, J., Ma, Y., Mi, Y., Cui, D., Ju, G., Macklin, W. B., & Jin, W. (2014) · Glia · doi:10.1002/glia.22649 · Cited by 53
Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques
Thomson, J. P., Hunter, J. M., Nestor, C. E., Dunican, D. S., Terranova, R., Moggs, J. G., & Meehan, R. R. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1080 · Cited by 51
Ludwig, A. K., Zhang, P., & Cardoso, M. C. (2016) · Frontiers in Genetics · doi:10.3389/fgene.2016.00115 · Cited by 56
Kernaleguen, M., Daviaud, C., Shen, Y., Bonnet, É., Renault, V., Deleuze, J., Mauger, F., & Tost, J. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7774-1_18 · Cited by 53
Quantification and mapping of DNA modifications
Dai, Y., Yuan, B., & Feng, Y. (2021) · RSC Chemical Biology · doi:10.1039/d1cb00022e · Cited by 54
Understanding posttraumatic stress disorder: insights from the methylome
Malan‐Müller, S., Seedat, S., & Hemmings, S. M. J. (2013) · Genes Brain & Behavior · doi:10.1111/gbb.12102 · Cited by 57
The Epigenomics of Embryonic Stem Cell Differentiation
Kraushaar, D. C., & Zhao, K. (2013) · International Journal of Biological Sciences · doi:10.7150/ijbs.7998 · Cited by 52
Khan, F. S., Ali, I., Afridi, U. K., Ishtiaq, M., & Mehmood, R. (2016) · Hepatology International · doi:10.1007/s12072-016-9743-4 · Cited by 52
TET enzymatic oxidation of 5-methylcytosine, 5-hydroxymethylcytosine and 5-formylcytosine
Cadet, J., & Wagner, J. R. (2013) · Mutation Research/Genetic Toxicology and Environmental Mutagenesis · doi:10.1016/j.mrgentox.2013.09.001 · Cited by 53
The role of chromatin modifiers in normal and malignant hematopoiesis
Napierala, J. S., & Dent, S. (2013) · Blood · doi:10.1182/blood-2012-10-451237 · Cited by 55
Almeida, R. D., Loose, M., Sottile, V., Matsa, E., Denning, C. N., Young, L. E., Johnson, A. D., Gering, M., & Ruzov, A. S. (2012) · Epigenetics · doi:10.4161/epi.19375 · Cited by 49
Hydroxymethylation of DNA influences nucleosomal conformation and stability in vitro
Mendonca, A., Chang, E. H., Liu, W., & Yuan, C. (2014) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2014.09.014 · Cited by 49
Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing
Zhang, L., Szulwach, K. E., Hon, G. C., Song, C., Park, B., Yu, M., Lu, X., Dai, Q., Wang, X., Street, C., et al. (2013) · Nature Communications · doi:10.1038/ncomms2527 · Cited by 51
The Impact of Nutrition on Differential Methylated Regions of the Genome
Parle‐McDermott, A., & Ozaki, M. (2011) · Advances in Nutrition · doi:10.3945/an.111.001008 · Cited by 50
5-Hydroxymethylcytosine: the many faces of the sixth base of mammalian DNA
Kriukienė, E., Tomkuvienė, M., & Klimašauskas, S. (2024) · Chemical Society Reviews · doi:10.1039/d3cs00858d · Cited by 50
Neri, F., Incarnato, D., Křepelová, A., Dettori, D., Rapelli, S., Maldotti, M., Parlato, C., Anselmi, F., Galvagni, F., & Oliviero, S. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv392 · Cited by 51
Epigenetic Basis of Neuronal and Synaptic Plasticity
Karpova, N. N., Sales, A. J., & Joca, S. R. L. (2016) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026616666160414124628 · Cited by 51
Hu, H., Shu, M., He, L., Yu, X., Liu, X., Lu, Y., Chen, Y., Miao, X., & Chen, X. (2017) · British Journal of Cancer · doi:10.1038/bjc.2016.457 · Cited by 50
Self-citationKubiura‐Ichimaru, M., Okano, M., Kimurâ, H., Kawamura, F., & Tada, M. (2012) · Chromosome Research · doi:10.1007/s10577-012-9317-9 · Cited by 47
TET proteins: on the frenetic hunt for new cytosine modifications
Delatte, B., & Fuks, F. (2013) · Briefings in Functional Genomics · doi:10.1093/bfgp/elt010 · Cited by 51
Li, R., Zhou, Y., Cao, Z., Liu, L., Wang, J., Chen, Z., Xing, W., Shi, C., Bai, J., Yuan, W., et al. (2017) · Stem Cell Reports · doi:10.1016/j.stemcr.2017.11.019 · Cited by 47
Shukla, A., Sehgal, M., & Singh, T. R. (2015) · Gene · doi:10.1016/j.gene.2015.03.075 · Cited by 46
Upadhyay, A. K., Horton, J. R., Zhang, X., & Cheng, X. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.08.003 · Cited by 46
Evaluation of single CpG sites as proxies of CpG island methylation states at the genome scale
Barrera, V., & Peinado, M. A. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks928 · Cited by 49
Zhang, X., Chen, X., Weirauch, M. T., Zhang, X., Burleson, J., Brandt, E. B., & Ji, H. (2018) · Current Zoology · doi:10.1093/eep/dvy020 · Cited by 47
Integrating DNA methylation dynamics into a framework for understanding epigenetic codes
Szulwach, K. E., & Jin, P. (2013) · BioEssays · doi:10.1002/bies.201300090 · Cited by 50
Recent advances in understanding the molecular pathogenesis of myelodysplastic syndromes
Kulasekararaj, A. G., Mohamedali, A. M., & Mufti, G. J. (2013) · British Journal of Haematology · doi:10.1111/bjh.12435 · Cited by 47
Label free detection of 5′hydroxymethylcytosine within CpG islands using optical sensors
Hawk, R., & Armani, A. M. (2014) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2014.10.041 · Cited by 44
Kaut, O., Kuchelmeister, K., Moehl, C., & Wüllner, U. (2018) · Journal of Chemical Neuroanatomy · doi:10.1016/j.jchemneu.2018.12.005 · Cited by 44
Decoding the role of TET family dioxygenases in lineage specification
Wu, X., Li, G., & Xie, R. (2018) · Epigenetics & Chromatin · doi:10.1186/s13072-018-0228-7 · Cited by 43
Establishment of epigenetic patterns in development
Leeb, M., & Wutz, A. (2012) · Chromosoma · doi:10.1007/s00412-012-0365-x · Cited by 46
New answers to old questions from genome-wide maps of DNA methylation in hematopoietic cells
Jeong, M., & Goodell, M. A. (2014) · Experimental Hematology · doi:10.1016/j.exphem.2014.04.008 · Cited by 45
Genome‐Wide Mapping of DNA Hydroxymethylation in Osteoarthritic Chondrocytes
Taylor, S. E. B., Li, Y. H., Wong, W. H., & Bhutani, N. (2015) · Arthritis & Rheumatology · doi:10.1002/art.39179 · Cited by 43
Computational analysis of DNA methylation from long-read sequencing
Fu, Y., Timp, W., & Sedlazeck, F. J. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-025-00822-5 · Cited by 43
Epigenetic control on cell fate choice in neural stem cells
Hu, X.-L., Wang, Y., & Shen, Q. (2012) · Protein & Cell · doi:10.1007/s13238-012-2916-6 · Cited by 45
TET2 Deficiency Inhibits Mesoderm and Hematopoietic Differentiation in Human Embryonic Stem Cells
Langlois, T., Monte-Mór, B. D. C. R., Lenglet, G., Droin, N. M., Marty, C., Couedic, J. P. L., Almire, C., Auger, N., Mercher, T., Delhommeau, F., et al. (2014) · Stem Cells · doi:10.1002/stem.1718 · Cited by 46
Intracellular Detection of Cytosine Incorporation in Genomic DNA by Using 5‐Ethynyl‐2′‐Deoxycytidine
Guan, L., van der Heijden, G. W., Bortvin, A. L., & Greenberg, M. M. (2011) · ChemBioChem · doi:10.1002/cbic.201100353 · Cited by 43
Chen, S., Dou, Y., Zhao, Z., Li, F., Su, J., Fan, C., & Song, S. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.6b00230 · Cited by 42
Kurian, J. R., Louis, S., Keen, K. L., Wolfe, A., Terasawa, E., & Levine, J. E. (2016) · Endocrinology · doi:10.1210/en.2016-1087 · Cited by 42
CRISPR-Mediated Epigenome Editing.
Enríquez, P. (2016) · Europe PMC (PubMed Central) · Cited by 41
Technical advances in global DNA methylation analysis in human cancers
Chowdhury, B., Cho, I., & Irudayaraj, J. (2017) · Journal of Biological Engineering · doi:10.1186/s13036-017-0052-9 · Cited by 42
Epigenetics and Cancer: A Comprehensive Review
Pathak, A., Tomar, S., & Pathak, S. (2023) · Asian Pacific Journal of Cancer Biology · doi:10.31557/apjcb.2023.8.1.75-89 · Cited by 41
Environmental Alterations of Epigenetics Prior to the Birth
Lo, C., & Zhou, F. (2014) · International review of neurobiology · doi:10.1016/b978-0-12-801311-3.00001-9 · Cited by 44
A conserved role for intragenic DNA methylation in alternative pre-mRNA splicing
Oberdoerffer, S. (2012) · Transcription · doi:10.4161/trns.19816 · Cited by 41
Gavin, D. P., & Akbarian, S. (2011) · Neurobiology of Disease · doi:10.1016/j.nbd.2011.12.008 · Cited by 42
Primoridal germ cell specification: a context-dependent cellular differentiation event
Günesdogan, U., Magnúsdóttir, E., & Surani, M. A. (2014) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0543 · Cited by 43
Juan, D., Perner, J., Pau, E. C. D. S., Marsili, S., Ochoa, D., Chung, H., Vingron, M., Rico, D., & Valencia, A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.01.008 · Cited by 41
Transcriptional and epigenetic mechanisms of cellular reprogramming to induced pluripotency
van den Hurk, M., Kenis, G., Bardy, C., van den Hove, D., Gage, F. H., Steinbusch, H. W. M., & Rutten, B. P. F. (2016) · Epigenomics · doi:10.2217/epi-2016-0032 · Cited by 44
Epigenetic Modulation of Chromatin States and Gene Expression by G-Quadruplex Structures
Reina, C., & Cavalieri, V. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21114172 · Cited by 43
Hong, T., Li, J., Guo, L., Cavalier, M., Wang, T., Dou, Y., de-la-Fuente, A. L. C., Fang, S., Guzman, A. G., Wohlan, K., et al. (2023) · Nature Aging · doi:10.1038/s43587-023-00505-y · Cited by 45
Self-citationEnzymatic Analysis of Tet Proteins: Key Enzymes in the Metabolism of DNA Methylation
Shen, L., & Zhang, Y. (2012) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-391940-3.00005-6 · Cited by 40
Whole-genome analysis of TET dioxygenase function in regulatory T cells
Yue, X., Samaniego‐Castruita, D., González‐Avalos, E., Li, X., Barwick, B. G., & Rao, A. (2021) · EMBO Reports · doi:10.15252/embr.202152716 · Cited by 37
Self-citationRegulation and function of mammalian DNA methylation patterns: a genomic perspective
Wu, H., Tao, J., & Sun, Y. E. (2012) · Briefings in Functional Genomics · doi:10.1093/bfgp/els011 · Cited by 40
TET proteins in cancer: Current ‘state of the art’
Rawłuszko-Wieczorek, A. A., Siera, A., & Jagodziński, P. P. (2015) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2015.07.008 · Cited by 40
Single Base Resolution Analysis of 5-Methylcytosine and 5-Hydroxymethylcytosine by RRBS and TAB-RRBS
Hahn, M. A., Li, A. X., Wu, X., & Pfeifer, G. P. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-1804-1_14 · Cited by 39
Antibodies specific for nucleic acid modifications
Feederle, R., & Schepers, A. (2017) · RNA Biology · doi:10.1080/15476286.2017.1295905 · Cited by 39
Wang, X., Song, S., Yong-sheng, W., Li, Y., Chen, T., Huang, Z., Liu, S., Dunwell, T. L., Pfeifer, G. P., Dunwell, J. M., et al. (2015) · Journal of Experimental Botany · doi:10.1093/jxb/erv372 · Cited by 39
Xu, L., Chen, Y., Chong, J. P. C., Fin, A., McCoy, L. S., Xu, J., Zhang, C., & Wang, D. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201406220 · Cited by 39
Choi, I., Kim, R., Lim, H., Kaestner, K. H., & Won, K. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-670 · Cited by 39
Green, B. B., Houseman, E. A., Johnson, K. C., Guerin, D. J., Armstrong, D. A., Christensen, B. C., & Marsit, C. J. (2016) · The FASEB Journal · doi:10.1096/fj.201600310r · Cited by 39
Aravind, L., Iyer, L. M., & Burroughs, A. M. (2022) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-122220-101119 · Cited by 40
Epigenetic features of the mouse trophoblast
Rugg‐Gunn, P. J. (2012) · Reproductive BioMedicine Online · doi:10.1016/j.rbmo.2012.01.012 · Cited by 38
Programmable Sensors of 5-Hydroxymethylcytosine
Kubik, G., Batke, S., & Summerer, D. (2015) · Journal of the American Chemical Society · doi:10.1021/ja506022t · Cited by 37
Chopra, P., Papale, L. A., White, A. T. J., Hatch, A., Brown, R. M., Garthwaite, M. A., Roseboom, P. H., Golos, T. G., Warren, S. T., & Alisch, R. S. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-131 · Cited by 37
Zhang, H., Liu, L., & Li, M. (2024) · ACS Sensors · doi:10.1021/acssensors.3c02328 · Cited by 37
Decottignies, A., & di Fagagna, F. D. (2011) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2011.09.003 · Cited by 37
Gadd45b and N -Methyl- d -Aspartate Induced DNA Demethylation in Postmitotic Neurons
Gavin, D. P., Kusumo, H., Sharma, R. P., Guizzetti, M., Guidotti, A., & Pandey, S. C. (2015) · Epigenomics · doi:10.2217/epi.15.12 · Cited by 38
Genome-wide assays that identify and quantify modified cytosines in human disease studies
Ulahannan, N., & Greally, J. M. (2015) · Epigenetics & Chromatin · doi:10.1186/1756-8935-8-5 · Cited by 36
Hong, T., Wang, T., Guo, P., Xing, X., Ding, F., Chen, Y., Wu, J., Ma, J., Wu, F., & Zhou, X. (2013) · Analytical Chemistry · doi:10.1021/ac4020676 · Cited by 36
The TET2 interactors and their links to hematological malignancies
Pan, F., Weeks, O. I., Yang, F., & Xu, M. (2015) · IUBMB Life · doi:10.1002/iub.1389 · Cited by 36
Tet-Assisted Bisulfite Sequencing (TAB-seq)
Yu, M., Han, D., Hon, G. C., & He, C. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7481-8_33 · Cited by 36
Jiang, Y., Liu, S., Chen, X. '., Cao, Y., & Tao, Y. (2012) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2012.12.003 · Cited by 36
Chromatin remodeling effects on enhancer activity
García-González, E. G., Escamilla-Del-Arenal, M., Arzate‐Mejía, R. G., & Targa, F. R. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2184-3 · Cited by 41
Andersen, G. B., & Tost, J. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7481-8_1 · Cited by 36
Song, G., Wang, G., Luo, X., Cheng, Y., Song, Q., Wan, J., Moore, C. D., Song, H., Jin, P., Qian, J. X., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-20950-w · Cited by 35
TET Proteins and 5-Methylcytosine Oxidation in the Immune SystemPreprint
Tsagaratou, A., & Rao, A. (2013) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2013.78.020248 · Cited by 36
Self-citationGao, F., Xia, Y., Wang, J., Luo, H., Gao, Z., Han, X., Zhang, J., Huang, X., Yao, Y., Lu, H., et al. (2013) · Epigenetics · doi:10.4161/epi.24280 · Cited by 34
Epigenetics, embryo quality and developmental potential
Beaujean, N. (2014) · Reproduction Fertility and Development · doi:10.1071/rd14309 · Cited by 34
Véron, N., & Peters, A. H. F. M. (2011) · Nature · doi:10.1038/473293a · Cited by 34
Developmental Epigenetics of the Murine Secondary Palate
Seelan, R. S., Mukhopadhyay, P., Pisano, M., & Greene, R. M. (2012) · ILAR Journal · doi:10.1093/ilar.53.3-4.240 · Cited by 34
Guanine- 5-carboxylcytosine base pairs mimic mismatches during DNA replication
Shibutani, T., Ito, S., Toda, M., Kanao, R., Collins, L. B., Shibata, M., Urabe, M., Koseki, H., Masuda, Y., Swenberg, J. A., et al. (2014) · Scientific Reports · doi:10.1038/srep05220 · Cited by 33
Nazor, K. L., Boland, M. J., Bibikova, M. V., Klotzle, B., Yu, M., Glenn-Pratola, V., Schell, J. P., Coleman, R. L., Cabral-da-Silva, M. C., Schmidt, U., et al. (2014) · Genomics · doi:10.1016/j.ygeno.2014.08.014 · Cited by 33
5‐Hydroxymethylcytosin, die sechste Base des Genoms
Münzel, M., Globisch, D., & Carell, T. (2011) · Angewandte Chemie · doi:10.1002/ange.201101547 · Cited by 33
5‐Hydroxymethylcytosine profiling from genomic and cell‐free DNA for colorectal cancers patients
Gao, P., Lin, S., Cai, M., Zhu, Y., Song, Y., Sui, Y., Lin, J., Liu, J., Lu, X., Zhong, Y., et al. (2019) · Journal of Cellular and Molecular Medicine · doi:10.1111/jcmm.14252 · Cited by 33
Stem cell fate determination through protein O-GlcNAcylation
Sheikh, M. A., Emerald, B. S., & Ansari, S. A. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.rev120.014915 · Cited by 34
Li, C., Dong, Y.-H., Zou, X., Luo, X., Shen, D., Hu, J., & Zhang, C. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.0c05419 · Cited by 33
Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers
Wei, A., & Wu, H. (2022) · Development · doi:10.1242/dev.182683 · Cited by 34
The potential of DNA modifications as biomarkers and therapeutic targets in oncology
Jankowska, A. M., Millward, C. L., & Caldwell, C. W. (2015) · Expert Review of Molecular Diagnostics · doi:10.1586/14737159.2015.1084229 · Cited by 34
Chávez, L., Huang, Y., Luong, K., Agarwal, S., Iyer, L. M., Pastor, W. A., Hench, V. K., Frazier‐Bowers, S. A., Korol, E., Liu, S., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419513111 · Cited by 33
Self-citationRole of TET2 Mutations in Myeloproliferative Neoplasms
Pronier, E., & Delhommeau, F. (2011) · Current Hematologic Malignancy Reports · doi:10.1007/s11899-011-0108-8 · Cited by 33
Cytosine modifications in neurodevelopment and diseases
Yao, B., & Jin, P. (2013) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-013-1433-y · Cited by 33
The Hunt for 5-Hydroxymethylcytosine: The Sixth Base
Song, C., & He, C. (2011) · Epigenomics · doi:10.2217/epi.11.74 · Cited by 32
Base-resolution profiling of active DNA demethylation using MAB-seq and caMAB-seq
Wu, H., Wu, X., & Zhang, Y. (2016) · Nature Protocols · doi:10.1038/nprot.2016.069 · Cited by 35
Li, Q.-Y., Xie, N., Xiong, J., Yuan, B., & Feng, Y. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b04833 · Cited by 32
Peng, V., Xing, X., Bando, J. K., Tršan, T., Luccia, B. D., Collins, P. L., Li, D., Wang, W.-L., Lee, H. J., Oltz, E. M., et al. (2022) · Nature Immunology · doi:10.1038/s41590-022-01164-8 · Cited by 33
Metadata
- Authors
- Pastor, W. A., Pape, U. J., Huang, Y., Henderson, H. R., Lister, R., Ko, M., McLoughlin, E. M., Brudno, Y., Mahapatra, S., Kapranov, P., Tahiliani, M., Daley, G. Q., Liu, X. S., Ecker, J. R., Milos, P. M., Agarwal, S., & Rao, A.
- Affiliations
- Boston Children's Hospital (US)
- La Jolla Institute for Immunology (US)
- Salk Institute for Biological Studies (US)
- Harvard University (US)
- Helicos Biosciences (United States) (US)
- Corresponding author
- Agarwal, Suneet
- Rao, Anjana
- ORCID
- Venue
- Nature
- Published
- 2011-05-08
- Volume
- 473
- Issue
- 7347
- Pages
- 394-397
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3124347
- OpenAlex
- W1981543052
- Cited by
- 804
- References
- 28
- Citations by year
- 2026: 9 · 2025: 29 · 2024: 23 · 2023: 21 · 2022: 32 · 2021: 33 · 2020: 24 · 2019: 39 · 2018: 41 · 2017: 58 · 2016: 78 · 2015: 64 · 2014: 84 · 2013: 118 · 2012: 96
- FWCI
- 43.02
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- UWA Profiles and Research Repository (UWA) (submittedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- Scholarworks@UNIST (Ulsan National Institute of Science and Technology) (submittedVersion)
- Funders
- National Science Foundation
- California Institute for Regenerative Medicine
- Leukemia and Lymphoma Society
- Harvard Catalyst (UL1-RR025758)
- California Institute of Regenerative Medicine
- National Institutes of Health
- National Heart, Lung, and Blood Institute (K08HL089150)
- National Institute on Drug Abuse (RC1DA028422)
- National Institute of Allergy and Infectious Diseases (R01AI044432)
- National Center for Research Resources (UL1RR025758)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD065812)
- 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 › Pluripotent Stem Cells Research
- Keywords
- 5-hydroxymethylcytosine, TET1, mouse embryonic stem cells, DNA demethylation, DNA methylation, H3K27me3, H3K4me3, transcriptional regulation, ChIP-seq, histone modifications, gene expression regulation
- MeSH terms
- Animals, Cell Line, Cytosine, Exons, Glucose, Periodic Acid, Promoter Regions, Genetic, Transcription, Genetic, Genome, Sequence Analysis, DNA, Gene Expression Regulation, Developmental, DNA Methylation, Biotinylation, Transcription Initiation Site, 5-Methylcytosine, Mice, Embryonic Stem Cells
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
