The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.
Genome-scale DNA methylation maps of pluripotent and differentiated cells
Open accessAbstract
DNA methylation is essential for normal development and has been implicated in many pathologies including cancer. Our knowledge about the genome-wide distribution of DNA methylation, how it changes during cellular differentiation and how it relates to histone methylation and other chromatin modifications in mammals remains limited. Here we report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput reduced representation bisulphite sequencing and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse embryonic stem cells, embryonic-stem-cell-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of embryonic-stem-cell-derived and primary cells reveals that 'weak' CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumours. More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.
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?
In the citing paper
“They provide better genomic coverage than 450K array, and can assess the genetic variants and allele-specific methylation beyond the preselected microarray probes.”
From Integrative Analysis of Multi-omics Data for Discovery and Functional Studies of Complex Human Diseases (2016) · cites this paper as Meissner et al., 2008
In the citing paper
“DNA methylation is thought to be involved in disease pathology through its influence on gene expression and cellular function5,6.”
From Methylome-wide change associated with response to electroconvulsive therapy in depressed patients (2021) · cites this paper as [6]
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
DNA methylation patterns and epigenetic memory
Bird, A. (2002) · Genes & Development · doi:10.1101/gad.947102 · Cited by 7,124
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
Self-citationJones, P. A., & Baylin, S. B. (2007) · Cell · doi:10.1016/j.cell.2007.01.029 · Cited by 4,515
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
Self-citationHeintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398
Frommer, M., McDonald, L. E., Millar, D. S., Collis, C. M., Watt, F., Grigg, G. W., Molloy, P. L., & Paul, C. L. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.5.1827 · Cited by 3,238
Weber, M., Hellmann, I., Stadler, M. B., Ramos, L., Pääbo, S., Rebhan, M., & Schübeler, D. (2007) · Nature Genetics · doi:10.1038/ng1990 · Cited by 2,297
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
Cokus, S. J., Feng, S.-H., Zhang, X.-Y., Chen, Z., Merriman, B., Haudenschild, C., Pradhan, S., Nelson, S., Pellegrini, M., & Jacobsen, S. (2008) · Nature · doi:10.1038/nature06745 · Cited by 2,278
Self-citationThe DNA methyltransferases of mammals
Bestor, T. H. (2000) · Human Molecular Genetics · doi:10.1093/hmg/9.16.2395 · Cited by 2,078
Stability and flexibility of epigenetic gene regulation in mammalian development
Reik, W. (2007) · Nature · doi:10.1038/nature05918 · Cited by 1,963
Flagged first, then by citations
Cited by
Sorted by citations
Items 601–700 of 1,010
Acetylation- and Methylation-Related Epigenetic Proteins in the Context of Their Targets
Javaid, N., & Choi, S. (2017) · Genes · doi:10.3390/genes8080196 · Cited by 97
RASSF1A uncouples Wnt from Hippo signalling and promotes YAP mediated differentiation via p73
Papaspyropoulos, A., Bradley, L., Thapa, A., Leung, C. Y., Toskas, K., Koennig, D., Pefani, D., Raso, C., Grou, C. P. O., Hamilton, G., et al. (2018) · Nature Communications · doi:10.1038/s41467-017-02786-5 · Cited by 90
Lu, V. M., Alvi, M. A., McDonald, K. L., & Daniels, D. J. (2019) · Journal of Neurosurgery Pediatrics · doi:10.3171/2018.9.peds18419 · Cited by 91
DNA methylation dynamics at transposable elements in mammals
Jansz, N. (2019) · Essays in Biochemistry · doi:10.1042/ebc20190039 · Cited by 95
Co-transcriptional regulation of alternative pre-mRNA splicing
Shukla, S., & Oberdoerffer, S. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.01.014 · Cited by 93
Optimized design and data analysis of tag-based cytosine methylation assays
Suzuki, M., Jing, Q., Lia, D., Pascual, M., McLellan, A. S., & Greally, J. M. (2010) · Genome biology · doi:10.1186/gb-2010-11-4-r36 · Cited by 89
Molecular Pathophysiology of Myelodysplastic Syndromes
Lindsley, R. C., & Ebert, B. L. (2013) · Annual Review of Pathology: Mechanisms of Disease · doi:10.1146/annurev-pathol-011811-132436 · Cited by 88
A Structural Perspective on Readout of Epigenetic Histone and DNA Methylation MarksPreprint
Patel, D. J. (2016) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a018754 · Cited by 91
Xi, Y., Bock, C., Müller, F., Sun, D., Meissner, A., & Li, W. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr668 · Cited by 91
Self-citationSuzuki, T., Shimizu, Y., Furuhata, E., Maeda, S., Kishima, M., Nishimura, H., Enomoto, S., Hayashizaki, Y., & Suzuki, H. (2017) · Blood Advances · doi:10.1182/bloodadvances.2017005710 · Cited by 87
Tao, Y., Xi, S., Shan, J., Maunakea, A. K., Che, A., Briones, V. R., Lee, E. Y., Geiman, T. M., Huang, J., Stephens, R. M., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1017000108 · Cited by 89
High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum
Xie, H., Wang, M., Bonaldo, M. F., Smith, C., Rajaram, V., Goldman, S., Tomita, T., & Soares, M. B. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp393 · Cited by 87
Genomic Analyses of Hormone Signaling and Gene Regulation
Cheung, E. C. W., & Kraus, W. L. (2010) · Annual Review of Physiology · doi:10.1146/annurev-physiol-021909-135840 · Cited by 86
Respuela, P., Nikolić, M., Tan, M., Frommolt, P., Zhao, Y., Wysocka, J., & Rada-Iglesias, Á. (2016) · Cell stem cell · doi:10.1016/j.stem.2015.09.010 · Cited by 81
Vinson, C., & Chatterjee, R. (2012) · Epigenomics · doi:10.2217/epi.12.55 · Cited by 89
Xu, H., Yi, B. A., Wu, H., Bock, C., Gu, H., Lui, K. O., Park, J. H. C., Shao, Y., Riley, A. K., Domian, I. J., et al. (2011) · Cell Research · doi:10.1038/cr.2011.171 · Cited by 86
Self-citationA genomic point-of-view on environmental factors influencing the human brain methylome
LaSalle, J. M. (2011) · Epigenetics · doi:10.4161/epi.6.7.16353 · Cited by 89
Recruitment and Biological Consequences of Histone Modification of H3K27me3 and H3K9me3
Kim, J. H., & Kim, H. (2012) · ILAR Journal · doi:10.1093/ilar.53.3-4.232 · Cited by 94
Large-Scale Identification of Coregulated Enhancer Networks in the Adult Human Brain
Vermunt, M. W., Reinink, P., Korving, J., de Bruijn, E., Creyghton, P. M., Başak, O., Geeven, G., Toonen, P. W., Lansu, N. R., Meunier, C., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.09.023 · Cited by 86
An Important Role for DNMT3A-Mediated DNA Methylation in Cardiomyocyte Metabolism and Contractility
Madsen, A., Höppner, G., Krause, J., Hirt, M. N., Laufer, S. D., Schweizer, M., Tan, W. L. W., Mosqueira, D., Anene-Nzelu, C. G., Lim, I. Y., et al. (2020) · Circulation · doi:10.1161/circulationaha.119.044444 · Cited by 91
Global and gene specific DNA methylation changes during zebrafish development
Fang, X., Corrales, J., Thornton, C., Scheffler, B. E., & Willett, K. L. (2013) · Comparative Biochemistry and Physiology Part B Biochemistry and Molecular Biology · doi:10.1016/j.cbpb.2013.07.007 · Cited by 88
Inactivation of Ezh2 Upregulates Gfi1 and Drives Aggressive Myc-Driven Group 3 Medulloblastoma
Vo, B. T., Li, C., Morgan, M. A., Theurillat, I., Finkelstein, D., Wright, S., Hyle, J. W., Smith, S. M. C., Fan, Y., Wang, Y., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.02.073 · Cited by 86
Adult porcine genome-wide DNA methylation patterns support pigs as a biomedical model
Schachtschneider, K. M., Madsen, O., Park, C., Rund, L. A., Groenen, M. A. M., & Schook, L. B. (2015) · BMC Genomics · doi:10.1186/s12864-015-1938-x · Cited by 84
Paul, T. A., Bies, J., Small, D., & Wolff, L. (2010) · Blood · doi:10.1182/blood-2009-07-233858 · Cited by 85
Tools and Strategies for Analysis of Genome-Wide and Gene-Specific DNA Methylation Patterns
Chatterjee, A., Rodger, E. J., Morison, I. M., Eccles, M. R., & Stockwell, P. A. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6685-1_15 · Cited by 84
Bonifacio, L. N., & Jarstfer, M. B. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012519 · Cited by 87
Girardot, M., Hirasawa, R., Kacem, S., Fritsch, L., Pontis, J., Kota, S. K., Filipponi, D., Fabbrizio, E., Sardet, C., Lohmann, F., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt884 · Cited by 85
Large-scale methylation domains mark a functional subset of neuronally expressed genesPreprint
Schroeder, D. I., Lott, P. C., Korf, I. F., & LaSalle, J. M. (2011) · Genome Research · doi:10.1101/gr.119131.110 · Cited by 87
Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins
LeRoy, G., Chepelev, I., DiMaggio, P. A., Blanco, M. A., Zee, B. M., Zhao, K., & Garcia, B. A. (2012) · Genome Biology · doi:10.1186/gb-2012-13-8-r68 · Cited by 84
Polycomb protein SCML2 facilitates H3K27me3 to establish bivalent domains in the male germline
Maezawa, S., Hasegawa, K., Yukawa, M., Kubo, N., Sakashita, A., Alavattam, K. G., Sin, H., Kartashov, A. V., Sasaki, H., Barski, A., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1804512115 · Cited by 84
Senner, C. E., Krueger, F., Oxley, D., Andrews, S., & Hemberger, M. (2012) · Stem Cells · doi:10.1002/stem.1249 · Cited by 89
LeDoux, M. S., Xiao, J., Rudzińska, M., Bastian, R. W., Wszołek, Z. K., van Gerpen, J. A., Puschmann, A., Momčilović, D., Vemula, S. R., & Zhao, Y. (2012) · Parkinsonism & Related Disorders · doi:10.1016/j.parkreldis.2012.02.001 · Cited by 83
Epigenetics in the hematologic malignancies
Fong, C. Y., Morison, J., & Dawson, M. A. (2014) · Haematologica · doi:10.3324/haematol.2013.092007 · Cited by 87
Promoter methylation confers kidney‐specific expression of the Klotho gene
Azuma, M., Koyama, D., Kikuchi, J., Yoshizawa, H., Dissayabutra, T., Shiizaki, K., Kuro‐o, M., Furukawa, Y., & Kusano, E. (2012) · The FASEB Journal · doi:10.1096/fj.12-211631 · Cited by 83
MMP-9 overexpression is associated with intragenic hypermethylation of MMP9 gene in melanoma
Falzone, L., Salemi, R., Travali, S., Scalisi, A., McCubrey, J. A., Candido, S., & Libra, M. (2016) · Aging · doi:10.18632/aging.100951 · Cited by 84
Ezura, Y., Sekiya, I., Koga, H., Muneta, T., & Noda, M. (2009) · Arthritis & Rheumatism · doi:10.1002/art.24472 · Cited by 83
The origins of glioma: E Pluribus Unum?
Siebzehnrübl, F. A., Reynolds, B. A., Vescovi, A. L., Steindler, D. A., & Deleyrolle, L. P. (2011) · Glia · doi:10.1002/glia.21143 · Cited by 91
Tackling the epigenome: challenges and opportunities for collaboration
Satterlee, J. S., Schübeler, D., & Ng, H. (2010) · Nature Biotechnology · doi:10.1038/nbt1010-1039 · Cited by 84
De Novo DNA Methylation Is Required to Restrict T Helper Lineage Plasticity
Thomas, R. M., Gamper, C. J., Ladle, B. H., Powell, J. D., & Wells, A. D. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.312785 · Cited by 83
SINE Retrotransposons Cause Epigenetic Reprogramming of Adjacent Gene Promoters
Estecio, M. R., Gallegos, J. J., Dekmezian, M. S., Lu, Y., Liang, S., & Issa, J. J. (2012) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-12-0351 · Cited by 82
Methods In Dna Methylation Profiling
Zuo, T., Tycko, B., Liu, T.-M., Lin, H.-J. L., & Huang, T. H. ‐. (2009) · Epigenomics · doi:10.2217/epi.09.31 · Cited by 83
DNA Methylation and Adult Neurogenesis
Jobe, E. M., & Zhao, X. (2016) · Brain Plasticity · doi:10.3233/bpl-160034 · Cited by 85
Environmental regulation of the neural epigenome
Caldji, C., Hellstrom, I. C., Zhang, T.-Y., Diorio, J., & Meaney, M. J. (2011) · FEBS Letters · doi:10.1016/j.febslet.2011.03.032 · Cited by 82
Epigenetics and DNA methylomic profiling in Alzheimer's disease and other neurodegenerative diseases
Roubroeks, J. A. Y., Smith, R. G., van den Hove, D., & Lunnon, K. (2017) · Journal of Neurochemistry · doi:10.1111/jnc.14148 · Cited by 81
Novel associations between blood DNA methylation and body mass index in middle-aged and older adults
Geurts, Y. M. G., Dugué, P., Joo, J. E., Makalic, E., Jung, C.-H., Guan, W., Nguyen, S., Grove, M. L., Wong, E. M., Hodge, A. M., et al. (2017) · International Journal of Obesity · doi:10.1038/ijo.2017.269 · Cited by 77
Hezroni, H., Sailaja, B. S., & Meshorer, E. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.266254 · Cited by 82
Krebs, A. R., Dessus-Babus, S., Burger, L., & Schübeler, D. (2014) · eLife · doi:10.7554/elife.04094 · Cited by 81
Histone Modifications and Chromatin Organization in Prostate Cancer
Chen, Z., Wang, L., Wang, Q., & Li, W. (2010) · Epigenomics · doi:10.2217/epi.10.31 · Cited by 82
Bae, J. M., Shin, S.-H., Kwon, H.-J., Park, S.-Y., Kook, M., Kim, Y., Cho, N., Kim, N., Kim, T., Kim, D., et al. (2011) · International Journal of Cancer · doi:10.1002/ijc.27369 · Cited by 81
Sørensen, A. L., Jacobsen, B. M., Reiner, A. H., Andersen, I. S., & Collas, P. (2010) · Molecular Biology of the Cell · doi:10.1091/mbc.e10-01-0018 · Cited by 83
Electrical Detection of Single Methylcytosines in a DNA Oligomer
Tsutsui, M., Matsubara, K., Ohshiro, T., Furuhashi, M., Taniguchi, M., & Kawai, T. (2011) · Journal of the American Chemical Society · doi:10.1021/ja203839e · Cited by 80
Reactivation of endogenous retroviral elements via treatment with DNMT- and HDAC-inhibitors
Daskalakis, M., Brocks, D., Sheng, Y.-H., Islam, S., Ressnerova, A., Assenov, Y., Milde, T., Oehme, I., Witt, O., Goyal, A., et al. (2018) · Cell Cycle · doi:10.1080/15384101.2018.1442623 · Cited by 90
Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing
Kunde‐Ramamoorthy, G., Coarfa, C., Laritsky, E., Kessler, N. J., Harris, R. A., Xu, M., Chen, R., Shen, L., Milosavljevic, A., & Waterland, R. A. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1325 · Cited by 80
Generation of Germline-Competent Rat Induced Pluripotent Stem Cells
Hamanaka, S., Yamaguchi, T., Kobayashi, T., Kato‐Itoh, M., Yamazaki, S., Sato, H., Umino, A., Wakiyama, Y., Arai, M., Sanbo, M., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022008 · Cited by 79
Human Endometrial DNA Methylome Is Cycle-Dependent and Is Associated With Gene Expression Regulation
Houshdaran, S., Zelenko, Z., Irwin, J. C., & Giudice, L. C. (2014) · Molecular Endocrinology · doi:10.1210/me.2013-1340 · Cited by 81
Epigenetic regulation of neurogenesis in the adult hippocampus
Covic, M., Karaca, E., & Lie, D. C. (2010) · Heredity · doi:10.1038/hdy.2010.27 · Cited by 83
Epigenetic Modulation of Stem Cells in Neurodevelopment: The Role of Methylation and Acetylation
Podobińska, M., Szabłowska‐Gadomska, I., Augustyniak, J., Sandvig, I., Sandvig, A., & Bużańska, L. (2017) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2017.00023 · Cited by 84
DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells
Choi, J., Clement, K., Huebner, A. J., Webster, J. O., Rose, C. M., Brumbaugh, J., Walsh, R. M., Lee, S., Savol, A. J., Etchegaray, J., et al. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.03.002 · Cited by 79
Self-citationFantastic Beasts and How To Sequence Them: Ecological Genomics for Obscure Model Organisms
Matz, M. V. (2017) · Trends in Genetics · doi:10.1016/j.tig.2017.11.002 · Cited by 87
Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells
Reitman, Z. J., Paolella, B. R., Bergthold, G., Pelton, K., Becker, S., Jones, R. E., Sinai, C. E., Malkin, H., Huang, Y., Grimmett, L., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11493-2 · Cited by 78
Prediction of Plant Height in Arabidopsis thaliana Using DNA Methylation Data
Hu, Y., Morota, G., Rosa, G. J. M., & Gianola, D. (2015) · Genetics · doi:10.1534/genetics.115.177204 · Cited by 79
Ehlert, T., Simon, P. D., & Moser, D. (2013) · Sports Medicine · doi:10.1007/s40279-012-0012-y · Cited by 84
Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome
Thomson, J. P., Lempiäinen, H., Hackett, J. A., Nestor, C. E., Müller, A., Bolognani, F., Oakeley, E. J., Schübeler, D., Terranova, R., Reinhardt, D., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-10-r93 · Cited by 77
Epigenetics: a new mechanism of regulation of heart failure?
Papait, R., Greco, C. M., Kunderfranco, P., Latronico, M. V. G., & Condorelli, G. (2013) · Basic Research in Cardiology · doi:10.1007/s00395-013-0361-1 · Cited by 78
Lelièvre, S. A. (2009) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2009.03.013 · Cited by 78
Nucleosomes protect DNA from DNA methylation in vivo and in vitro
Felle, M., Hoffmeister, H., Rothammer, J., Fuchs, A., Exler, J. H., & Längst, G. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr263 · Cited by 74
Zhao, M., Chen, H., Liu, Q., Shao, N., Sayed, N., Wo, H.-T., Zhang, J. Z., Ong, S., Liu, C., Kim, Y., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1708991114 · Cited by 78
Non-canonical functions of the DNA methylome in gene regulation
Reddington, J. P., Pennings, S., & Meehan, R. R. (2013) · Biochemical Journal · doi:10.1042/bj20121585 · Cited by 81
DNA Methylation in Skeletal Muscle Stem Cell Specification, Proliferation, and Differentiation
Laker, R. C., & Ryall, J. G. (2016) · Stem Cells International · doi:10.1155/2016/5725927 · Cited by 77
Stem cells in tissues, organoids, and cancers
Wang, X. (2019) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-019-03199-x · Cited by 80
Campbell, K. A., Colacino, J. A., Puttabyatappa, M., Dou, J., Elkin, E. R., Hammoud, S. S., Domino, S. E., Dolinoy, D. C., Goodrich, J. M., Loch-Caruso, R. K., et al. (2023) · Communications Biology · doi:10.1038/s42003-023-04623-6 · Cited by 84
The use of small molecules in somatic-cell reprogramming
Alexander Joel Federation, Bradner, J. E., & Meissner, A. (2013) · Trends in Cell Biology · doi:10.1016/j.tcb.2013.09.011 · Cited by 74
Self-citationDNA methylation in embryonic stem cells
Altun, G., Loring, J. F., & Laurent, L. C. (2009) · Journal of Cellular Biochemistry · doi:10.1002/jcb.22374 · Cited by 79
The cell cycle and pluripotency
Hindley, C. J., & Philpott, A. (2013) · Biochemical Journal · doi:10.1042/bj20121627 · Cited by 81
DNA methylation in obesity and type 2 diabetes
de Mello, V. D., Pulkkinen, L., Lalli, M., Kolehmainen, M., Pihlajamäki, J., & Uusitupa, M. I. J. (2014) · Annals of Medicine · doi:10.3109/07853890.2013.857259 · Cited by 78
Becker, K. A., Stein, J. L., Lian, J. B., van Wijnen, A. J., & Stein, G. S. (2009) · Journal of Cellular Physiology · doi:10.1002/jcp.21925 · Cited by 76
PPM1D mutations silence NAPRT gene expression and confer NAMPT inhibitor sensitivity in glioma
Fons, N. R., Sundaram, R. K., Breuer, G. A., Peng, S., McLean, R. L., Kalathil, A., Schmidt, M. S., Carvalho, D. M., Mackay, A. G., Jones, C., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11732-6 · Cited by 77
The Principles and Applications of High-Throughput Sequencing Technologies
Lee, J.-Y. (2023) · Development & Reproduction · doi:10.12717/dr.2023.27.1.9 · Cited by 81
Carrière, L., Graziani, S., Alibert, O., Ghavi-Helm, Y., Boussouar, F., Humbertclaude, H., Jounier, S., Aude, J.-C., Keime, C., Murvai, J., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr737 · Cited by 75
Cooperative DNA and histone binding by Uhrf2 links the two major repressive epigenetic pathways
Pichler, G., Wolf, P., Schmidt, C. S., Meilinger, D., Schneider, K., Frauer, C., Fellinger, K., Rottach, A., & Leonhardt, H. (2011) · Journal of Cellular Biochemistry · doi:10.1002/jcb.23185 · Cited by 76
Shifting behaviour: epigenetic reprogramming in eusocial insects
Patalano, S., Hore, T. A., Reik, W., & Sumner, S. (2012) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2012.02.005 · Cited by 76
Epigenetics: deciphering how environmental factors may modify autoimmune type 1 diabetes
MacFarlane, A. J., Strom, A., & Scott, F. W. (2009) · Mammalian Genome · doi:10.1007/s00335-009-9213-6 · Cited by 78
Early demethylation of non-CpG, CpC-rich, elements in the myogenin 5’-flanking region
Fuso, A., Ferraguti, G., Grandoni, F., Ruggeri, R., Scarpa, S., Ström, R., & Lucarelli, M. (2010) · Cell Cycle · doi:10.4161/cc.9.19.13193 · Cited by 75
McCabe, M. T., Lee, E. K., & Vertino, P. M. (2008) · Cancer Research · doi:10.1158/0008-5472.can-08-3274 · Cited by 75
Jeltsch, A. (2010) · Science · doi:10.1126/science.1190738 · Cited by 77
An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding
Mahony, S., Edwards, M. D., Mazzoni, E. O., Sherwood, R. I., Kakumanu, A., Morrison, C. A., Wichterle, H., & Gifford, D. K. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003501 · Cited by 75
DNA methylation dynamics in the hepatic CYP3A4 gene promoter
Kacevska, M., Ivanov, M., Wyss, A., Kasela, S., Milani, L. A., Rane, A., & Ingelman‐Sundberg, M. (2012) · Biochimie · doi:10.1016/j.biochi.2012.07.013 · Cited by 74
Hilakivi‐Clarke, L., de Assis, S., & Wärri, A. M. (2013) · Journal of Mammary Gland Biology and Neoplasia · doi:10.1007/s10911-013-9274-8 · Cited by 75
Carrió, E., Díez-Villanueva, A., Lois, S., Mallona, I., Cases, I., Forn, M., Peinado, M. A., & Suelves, M. (2015) · Stem Cells · doi:10.1002/stem.1998 · Cited by 72
Cancer-Related Epigenome Changes Associated with Reprogramming to Induced Pluripotent Stem Cells
Ohm, J. E., Mali, P., Neste, L. V., Berman, D. M., Liang, L., Pandiyan, K., Briggs, K. J., Zhang, W., Argani, P., Simons, B. W., et al. (2010) · Cancer Research · doi:10.1158/0008-5472.can-10-1361 · Cited by 71
Jeltsch, A., Broche, J., & Bashtrykov, P. (2018) · Genes · doi:10.3390/genes9110566 · Cited by 79
Defining CD4 T Cell Memory by the Epigenetic Landscape of CpG DNA Methylation
Komori, H. K., Hart, T., LaMere, S. A., Chew, P. V., & Salomon, D. R. (2015) · The Journal of Immunology · doi:10.4049/jimmunol.1401162 · Cited by 74
Jelı́nek, J., Liang, S., Lu, Y., He, R. L., Ramagli, L. S., Shpall, E. J., Estecio, M. R., & Issa, J. J. (2012) · Epigenetics · doi:10.4161/epi.22552 · Cited by 71
Early nutrition and epigenetic programming: chasing shadows
Attig, L., Gabory, A., & Junien, C. (2010) · Current Opinion in Clinical Nutrition & Metabolic Care · doi:10.1097/mco.0b013e328338aa61 · Cited by 76
Kwan, K. Y., Shen, J., & Corey, D. P. (2014) · Stem Cell Reports · doi:10.1016/j.stemcr.2014.11.001 · Cited by 73
Base-Resolution Maps of 5-Methylcytosine and 5-Hydroxymethylcytosine in Dahl S Rats
Liu, Y., Liu, P., Yang, C., Cowley, A. W., & Liang, M. (2014) · Hypertension · doi:10.1161/hypertensionaha.113.02637 · Cited by 73
Epigenetic regulation of satellite cell activation during muscle regeneration
Dilworth, F. J., & Blais, A. (2011) · Stem Cell Research & Therapy · doi:10.1186/scrt59 · Cited by 77
Gavery, M. R., Nichols, K. M., Goetz, G., Middleton, M. A., & Swanson, P. (2018) · G3 Genes Genomes Genetics · doi:10.1534/g3.118.200458 · Cited by 72
Veazey, K. J., Carnahan, M. N., Müller, D., Miranda, R. C., & Golding, M. C. (2013) · Alcoholism Clinical and Experimental Research · doi:10.1111/acer.12080 · Cited by 74
Deciphering the Epigenetic Code: An Overview of DNA Methylation Analysis Methods
Umer, M., & Herceg, Z. (2012) · Antioxidants and Redox Signaling · doi:10.1089/ars.2012.4923 · Cited by 78
Metadata
- Authors
- Meissner, A., Mikkelsen, T. S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B. E., Nusbaum, C., Jaffe, D. B., Gnirke, A., Jaenisch, R., & Lander, E. S.
- Affiliations
- Whitehead Institute for Biomedical Research (US)
- Broad Institute (US)
- Corresponding author
- Jaenisch, Rudolf
- Lander, Eric S.
- ORCID
- Venue
- Nature
- Published
- 2008-07-06
- Volume
- 454
- Issue
- 7205
- Pages
- 766-770
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2896277
- OpenAlex
- W2161224111
- Cited by
- 2,536
- References
- 30
- Citations by year
- 2026: 40 · 2025: 53 · 2024: 74 · 2023: 81 · 2022: 73 · 2021: 124 · 2020: 91 · 2019: 110 · 2018: 102 · 2017: 141 · 2016: 138 · 2015: 192 · 2014: 194 · 2013: 218 · 2012: 230
- FWCI
- 91.64
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Broad Institute
- National Human Genome Research Institute (R01HG004401, U54HG003067)
- 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
- DNA methylation, embryonic stem cells, cell differentiation, CpG islands, histone methylation, epigenetic profiling, neural cells, hypermethylation, transposable elements, conserved non-coding elements, mice, cancer epigenetics, regenerative medicine
- MeSH terms
- Animals, Cell Differentiation, Cells, Cultured, Fibroblasts, Histones, Male, Neurons, Genome, Conserved Sequence, CpG Islands, DNA Methylation, Genomics, Pluripotent Stem Cells, 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
