The DOI matches its Crossref record; 50 of the 50 references it cites were found in a registry or an index.
Human DNA methylomes at base resolution show widespread epigenomic differences
Open accessAbstract
DNA cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease. Here we present the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA-protein interaction for several key regulatory factors. Widespread differences were identified in the composition and patterning of cytosine methylation between the two genomes. Nearly one-quarter of all methylation identified in embryonic stem cells was in a non-CG context, suggesting that embryonic stem cells may use different methylation mechanisms to affect gene regulation. Methylation in non-CG contexts showed enrichment in gene bodies and depletion in protein binding sites and enhancers. Non-CG methylation disappeared upon induced differentiation of the embryonic stem cells, and was restored in induced pluripotent stem cells. We identified hundreds of differentially methylated regions proximal to genes involved in pluripotency and differentiation, and widespread reduced methylation levels in fibroblasts associated with lower transcriptional activity. These reference epigenomes provide a foundation for future studies exploring this key epigenetic modification in human disease and development.
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
“In most somatic tissues, the majority (>80%) of CpGs in the genome are methylated, with the exception of CGIs, and other gene regulatory sequences that show reduced 5mC levels (3).”
From Dynamic DNA methylation: In the right place at the right time (2018) · cites this paper as [3]
In the citing paper
“In PMD associated tissues such cultured fibroblasts, genes located in PMDs are both lowly expressed and methylated (3).”
From Dynamic DNA methylation: In the right place at the right time (2018) · cites this paper as [3]
In the citing paper
“Human embryonic stem cells (hESC) and mammalian brain tissues contain abundant non-CG methylation (5mCH, where H equals A, C or T) although the underlying three-base DNA sequence context (5mCAG vs. 5mCAC, respectively) is distinct (3, 13).”
From Dynamic DNA methylation: In the right place at the right time (2018) · cites this paper as [3]
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
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Embryonic Stem Cell Lines Derived from Human Blastocysts
Thomson, J. A., Itskovitz‐Eldor, J., Shapiro, S. S., Waknitz, M. A., Swiergiel, J. J., Marshall, V. S., & Jones, J. M. (1998) · Science · doi:10.1126/science.282.5391.1145 · Cited by 15,947
Self-citationBioconductor: open software development for computational biology and bioinformatics
Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 12,082
Okano, M., Bell, D. W., Haber, D. A., & Li, E. (1999) · Cell · doi:10.1016/s0092-8674(00)81656-6 · Cited by 6,143
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
Jones, P. A., & Baylin, S. B. (2007) · Cell · doi:10.1016/j.cell.2007.01.029 · Cited by 4,515
Targeted mutation of the DNA methyltransferase gene results in embryonic lethality
Li, E., Bestor, T. H., & Jaenisch, R. (1992) · Cell · doi:10.1016/0092-8674(92)90611-f · Cited by 3,984
Heintzman, 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
Self-citationGenome-Wide Mapping of in Vivo Protein-DNA Interactions
Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927
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
Cited by
Sorted by citations
Items 901–1,000 of 1,035
Targeted DNA Methylation Analysis by Next-generation Sequencing
Masser, D. R., Stanford, D. R., & Freeman, W. M. (2015) · Journal of Visualized Experiments · doi:10.3791/52488 · Cited by 95
Epigenetic regulation in neural crest development
Hu, N., Strobl‐Mazzulla, P. H., & Bronner-Fraser, M. E. (2014) · Developmental Biology · doi:10.1016/j.ydbio.2014.09.034 · Cited by 95
De novo DNA demethylation and noncoding transcription define active intergenic regulatory elementsPreprint
Schlesinger, F. J., Smith, A. D., Gingeras, T., Hannon, G. J., & Hodges, E. C. (2013) · Genome Research · doi:10.1101/gr.157271.113 · Cited by 96
Clark, C., Palta, P., Joyce, C. J., Scott, C., Grundberg, E., Deloukas, P., Palotie, A. V., & Coffey, A. J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0050233 · Cited by 94
Epigenetic alterations underlying autoimmune diseases
Aslani, S., Mahmoudi, M., Karami, J., Jamshidi, A., Malekshahi, Z., & Nicknam, M. H. (2016) · Autoimmunity · doi:10.3109/08916934.2015.1134511 · Cited by 94
Genome-wide epigenomic profiling for biomarker discovery
Dirks, R. A. M., Stunnenberg, H. G., & Marks, H. (2016) · Clinical Epigenetics · doi:10.1186/s13148-016-0284-4 · Cited by 94
Gene body DNA methylation conspires with H3K36me3 to preclude aberrant transcription
Teissandier, A., & Bourc’his, D. (2017) · The EMBO Journal · doi:10.15252/embj.201796812 · Cited by 94
DNA methylation dynamics at transposable elements in mammals
Jansz, N. (2019) · Essays in Biochemistry · doi:10.1042/ebc20190039 · Cited by 95
Lu, X., Zhang, Y., Wang, L., Wang, L., Wang, H., Xu, Q., Xiang, Y., Chen, C., Kong, F., Xia, W., et al. (2021) · Science Advances · doi:10.1126/sciadv.abi6178 · Cited by 94
DNA methylation in schizophrenia: progress and challenges of epigenetic studies
Nishioka, M., Bundo, M., Kasai, K., & Iwamoto, K. (2012) · Genome Medicine · doi:10.1186/gm397 · Cited by 94
Dissecting DNA hypermethylation in cancer
Estecio, M. R., & Issa, J. J. (2010) · FEBS Letters · doi:10.1016/j.febslet.2010.12.001 · Cited by 94
Metzger, D. C. H., & Schulte, P. M. (2016) · Marine Genomics · doi:10.1016/j.margen.2016.01.004 · Cited by 94
Noh, K., Wang, H., Kim, H. R., Wenderski, W., Fang, F., Li, C. H., Dewell, S. B., Hughes, S. H., Melnick, A. M., Patel, D. J., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.05.017 · Cited by 93
Evolutionary Consequences of DNA Methylation on the GC Content in Vertebrate Genomes
Mugal, C. F., Arndt, P. F., Holm, L., & Ellegren, H. (2015) · G3 Genes Genomes Genetics · doi:10.1534/g3.114.015545 · Cited by 93
Glinsky, G. V. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv081 · Cited by 93
MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma
Wang, D., Hashimoto, H., Zhang, X., Barwick, B. G., Lonial, S., Boise, L., Vertino, P. M., & Cheng, X. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1184 · Cited by 93
Chen, L., Huang, M., Plummer, J., Pan, J., Jiang, Y. Y., Yang, Q., Silva, T. C., Gull, N., Chen, S., Ding, L., et al. (2019) · Gut · doi:10.1136/gutjnl-2019-318325 · Cited by 93
Cell division drives DNA methylation loss in late-replicating domains in primary human cells
Endicott, J. L., Nolte, P. A., Shen, H., & Laird, P. W. (2022) · Nature Communications · doi:10.1038/s41467-022-34268-8 · Cited by 93
Lewandowska, J., & Bartoszek, A. (2011) · Mutagenesis · doi:10.1093/mutage/ger019 · Cited by 93
Advances in Genome-Wide DNA Methylation Analysis
Gupta, R., Nagarajan, A. G., & Wajapeyee, N. (2010) · BioTechniques · doi:10.2144/000113493 · Cited by 93
Epigenetic regulation of colon cancer and intestinal stem cells
Hammoud, S. S., Cairns, B. R., & Jones, D. A. (2013) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2013.01.007 · Cited by 93
Epigenetic mechanisms and the relationship to childhood asthma
Kabesch, M., Michel, S., & Tost, J. (2010) · European Respiratory Journal · doi:10.1183/09031936.00019310 · Cited by 93
Predictors and Consequences of Global DNA Methylation in Cord Blood and at Three Years
Herbstman, J. B., Wang, S., Perera, F. P., Lederman, S. A., Vishnevetsky, J., Rundle, A., Hoepner, L., Qu, L., & Tang, D. L. (2013) · PLoS ONE · doi:10.1371/journal.pone.0072824 · Cited by 93
Jung, M., Peterson, H., Chávez, L., Kahlem, P., Lehrach, H., Vilo, J., & Adjaye, J. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010709 · Cited by 92
5-Hydroxymethylcytosine – the elusive epigenetic mark in mammalian DNA
Kriukienė, E., Liutkevičiūtė, Z., & Klimašauskas, S. (2012) · Chemical Society Reviews · doi:10.1039/c2cs35104h · Cited by 92
Marked Global DNA Hypomethylation Is Associated with Constitutive PD-L1 Expression in Melanoma
Chatterjee, A., Rodger, E. J., Ahn, A., Stockwell, P. A., Parry, M. F., Motwani, J., Gallagher, S. J., Shklovskaya, E., Tiffen, J. C., Eccles, M. R., et al. (2018) · iScience · doi:10.1016/j.isci.2018.05.021 · Cited by 92
Lanata, C. M., Chung, S. A., & Criswell, L. A. (2018) · Lupus Science & Medicine · doi:10.1136/lupus-2018-000285 · Cited by 92
The Chromatin Fingerprint of Gene Enhancer Elements
Zentner, G. E., & Scacheri, P. C. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.r111.296491 · Cited by 92
Almstrup, K., Nielsen, J. E., Mlynarska, O., Jansen, M., Jørgensen, A., Skakkebæk, N. E., & Meyts, E. R. (2010) · British Journal of Cancer · doi:10.1038/sj.bjc.6605880 · Cited by 92
Regulation of DNA Methylation Patterns by CK2-Mediated Phosphorylation of Dnmt3a
Deplus, R., Blanchon, L., Rajavelu, A., Boukaba, A., Defrance, M., Luciani, J., Rothé, F., Dedeurwaerder, S., Denis, H., Brinkman, A. B., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.06.048 · Cited by 92
O’Connell, K. S., McGregor, N. W., Löchner, C., Emsley, R. A., & Warnich, L. (2018) · Molecular and Cellular Neuroscience · doi:10.1016/j.mcn.2018.02.010 · Cited by 92
Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos
Lee, H. J., Lowdon, R. F., Maricque, B. B., Zhang, B., Stevens, M. W., Li, D., Johnson, S. L., & Wang, T. (2015) · Nature Communications · doi:10.1038/ncomms7315 · Cited by 92
Xi, Y., Bock, C., Müller, F., Sun, D., Meissner, A., & Li, W. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr668 · Cited by 91
Salilew‐Wondim, D., Fournier, É., Hoelker, M., Saeed‐Zidane, M., Tholen, E., Looft, C., Neuhoff, C., Besenfelder, U., Havlicek, V., Rings, F., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0140467 · Cited by 91
Exploring the extent and scope of epigenetic inheritance
Radford, E. J. (2018) · Nature Reviews Endocrinology · doi:10.1038/s41574-018-0005-5 · Cited by 91
Long-read sequencing in the era of epigenomics and epitranscriptomics
Lucas, M. C., & Novoa, E. M. (2023) · Nature Methods · doi:10.1038/s41592-022-01724-8 · Cited by 91
Klug, M., Heinz, S., Gebhard, C., Schwarzfischer, L., Krause, S. W., Andreesen, R., & Rehli, M. (2010) · Genome biology · doi:10.1186/gb-2010-11-6-r63 · Cited by 91
Sati, S., Tanwar, V. S., Kumar, K. A., Patowary, A., Jain, V. K., Ghosh, S., Ahmad, S., Singh, M., Reddy, S., Chandak, G. R., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0031621 · Cited by 90
Edgar, R. D., Tan, P. P. C., Portales-Casamar, É., & Pavlidis, P. (2014) · Epigenetics & Chromatin · doi:10.1186/1756-8935-7-28 · Cited by 90
Exposing the DNA methylome iceberg
Ndlovu, ’. N., Denis, H., & Fuks, F. (2011) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2011.03.002 · Cited by 90
Li, J., Harris, R. A., Cheung, S. W., Coarfa, C., Jeong, M., Goodell, M. A., White, L. D., Patel, A., Kang, S.-H. L., Shaw, C. A., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002692 · Cited by 90
The impact of next-generation sequencing on the DNA methylation–based translational cancer research
Soto, J. A., Rodríguez‐Antolín, C., Vallespín, E., de Castro, J., & de Cáceres, I. I. (2015) · Translational research · doi:10.1016/j.trsl.2015.11.003 · Cited by 90
Rodríguez‐Paredes, M., Bormann, F., Raddatz, G., Gutekunst, J., Lucena-Porcel, C., Köhler, F., Wurzer, E., Schmidt, K., Gallinat, S., Wenck, H., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03025-1 · Cited by 90
Invited Review: Epigenetics in neurodevelopment
Salinas, R. D., Connolly, D. R., & Song, H. (2020) · Neuropathology and Applied Neurobiology · doi:10.1111/nan.12608 · Cited by 90
Covering Your Bases: Inheritance of DNA Methylation in Plant Genomes
Niederhuth, C. E., & Schmitz, R. J. (2013) · Molecular Plant · doi:10.1093/mp/sst165 · Cited by 90
Szyf, M. (2011) · Toxicological Sciences · doi:10.1093/toxsci/kfr024 · Cited by 90
A 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
Analyzing the cancer methylome through targeted bisulfite sequencing
Lee, E.-J., Luo, J., Wilson, J. M., & Shi, H. (2012) · Cancer Letters · doi:10.1016/j.canlet.2012.10.040 · Cited by 89
Nasu, K., Kawano, Y., Tsukamoto, Y., Takano, M., Takai, N., Li, H., Furukawa, Y., Abe, W., Moriyama, M., & Narahara, H. (2011) · Journal of obstetrics and gynaecology research · doi:10.1111/j.1447-0756.2011.01663.x · Cited by 89
Understanding the Relevance of DNA Methylation Changes in Immune Differentiation and Disease
de la Calle‐Fabregat, C., Morante-Palacios, O., & Ballestar, E. (2020) · Genes · doi:10.3390/genes11010110 · Cited by 89
Yi, M., Tan, Y., Wang, L., Cai, J., Li, X., Zeng, Z., Xiong, W., Li, X., Li, X., Tan, P., et al. (2020) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-020-03539-2 · Cited by 89
The histone variant H2A.Z is an important regulator of enhancer activity
Brunelle, M., Nordell-Markovits, A., Rodrigue, S., Lupien, M., Jacques, P., & Gévry, N. Y. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv825 · Cited by 90
Senner, C. E., Krueger, F., Oxley, D., Andrews, S., & Hemberger, M. (2012) · Stem Cells · doi:10.1002/stem.1249 · Cited by 89
Epigenetic layers and players underlying neurodevelopment
LaSalle, J. M., Powell, W. T., & Yasui, D. H. (2013) · Trends in Neurosciences · doi:10.1016/j.tins.2013.05.001 · Cited by 89
El‐Maarri, O., Walier, M., Behne, F., van Üüm, J., Singer, H., Diaz-Lacava, A. N., Nüsgen, N., Niemann, B., Watzka, M., REINSBERG, J., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016252 · Cited by 89
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
Metabolic Memory and Chronic Diabetes Complications: Potential Role for Epigenetic Mechanisms
Intine, R. V. A., & Sarras, M. P. (2012) · Current Diabetes Reports · doi:10.1007/s11892-012-0302-7 · Cited by 89
Role of DNMT3B in the regulation of early neural and neural crest specifiers
Martins‐Taylor, K., Schroeder, D. I., LaSalle, J. M., Lalande, M., & Xu, R.-H. (2012) · Epigenetics · doi:10.4161/epi.7.1.18750 · Cited by 89
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
Vinson, C., & Chatterjee, R. (2012) · Epigenomics · doi:10.2217/epi.12.55 · Cited by 89
Cai, Y., Tsai, H.-C., Yen, R.-W. C., Zhang, Y. W., Kong, X., Wang, W., Xia, L., & Baylin, S. B. (2017) · Genome Research · doi:10.1101/gr.208108.116 · Cited by 89
Sofo, V., Götte, M., Laganà, A. S., Salmeri, F. M., Triolo, O., Sturlese, E., Retto, G., Alfa, M., Granese, R., & Abrão, M. S. (2015) · Archives of Gynecology and Obstetrics · doi:10.1007/s00404-015-3739-5 · Cited by 88
Epigenetics in fertilization and preimplantation embryo development
Rivera, R. M., & Ross, J. W. (2013) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2013.02.001 · Cited by 88
DNA methylation abnormalities in atherosclerosis
Tabaei, S., & Tabaee, S. S. (2019) · Artificial Cells Nanomedicine and Biotechnology · doi:10.1080/21691401.2019.1617724 · Cited by 88
George, J. W., Fan, H., Johnson, B. K., Carpenter, T. J., Foy, K. K., Chatterjee, A., Patterson, A. L., Koeman, J. M., Adams, M., Madaj, Z., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.11.077 · Cited by 88
Li, R., Hu, F., Li, B., Zhang, Y., Chen, M., Fan, T., & Wang, T. (2020) · Scientific Reports · doi:10.1038/s41598-020-64975-5 · Cited by 88
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
Wilms Tumor Chromatin Profiles Highlight Stem Cell Properties and a Renal Developmental Network
Aiden, A. P., Rivera, M. N., Rheinbay, E., Ku, M., Coffman, E. J., Truong, T. T., Vargas, S. O., Lander, E. S., Haber, D. A., & Bernstein, B. (2010) · Cell stem cell · doi:10.1016/j.stem.2010.03.016 · Cited by 88
Zheng, X., Zhao, Q. C., Wu, H., Li, W., Wang, H., Meyer, C. A., Qin, Q., Xu, H., Zang, C., Jiang, P., et al. (2014) · Genome biology · doi:10.1186/preaccept-9737754001327268 · Cited by 88
Extensive sex differences at the initiation of genetic recombination
Brick, K., Thibault-Sennett, S., Smagulova, F. O., Lam, K.-W. G., Pu, Y., Pratto, F., Camerini‐Otero, R. D., & Petukhova, G. V. (2018) · Nature · doi:10.1038/s41586-018-0492-5 · Cited by 88
Fantastic 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
Price, A. J., Collado‐Torres, L., Ivanov, N. A., Xia, W. T., Burke, E. E., Shin, J. H., Tao, R., Ma, L., Jia, Y., Hyde, T. M., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1805-1 · Cited by 88
Multi-Omics Approaches in Immunological Research
Chu, X., Zhang, B., Koeken, V. A. C. M., Gupta, M. K., & Li, Y. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.668045 · Cited by 87
Wang, J., Xia, Y., Li, L., Gong, D., Yao, Y., Luo, H., Lu, H., Yi, N., Wu, H., Zhang, X., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-11 · Cited by 87
Research progress in allele-specific expression and its regulatory mechanisms
Gaur, U., Li, K., Mei, S., & Liu, G. (2013) · Journal of Applied Genetics · doi:10.1007/s13353-013-0148-y · Cited by 88
Epigenomic plasticity within populations: its evolutionary significance and potential
Johnson, L. J., & Tricker, P. J. (2010) · Heredity · doi:10.1038/hdy.2010.25 · Cited by 87
Jjingo, D., Conley, A. B., Wang, J., Mariño‐Ramírez, L., Lunyak, V. V., & Jordan, I. K. (2014) · Mobile DNA · doi:10.1186/1759-8753-5-14 · Cited by 89
A unique family of Mrr-like modification-dependent restriction endonucleases
Zheng, Y., Cohen-Karni, D., Xu, D., Chin, H. G., Wilson, G. G., Pradhan, S., & Roberts, R. J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq327 · Cited by 87
Prazeres, H., Torres, J., Rodrigues, F., Pinto, M. T., Pastoriza, M. C., Gomes, D., Cameselle‐Teijeiro, J., Vidal, A., Martins, T., Sobrinho-Simões, M. A., et al. (2010) · Oncogene · doi:10.1038/onc.2010.512 · Cited by 87
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
Sun, Z., Dai, N., Borgaro, J. G., Quimby, A., Sun, D., Junior, I. R. C., Zheng, Y., Zhu, Z., & Guan, S. (2015) · Molecular Cell · doi:10.1016/j.molcel.2014.12.035 · Cited by 86
Chen, J., Zhang, D., Yan, W., Yang, D., & Shen, B. (2013) · BioMed Research International · doi:10.1155/2013/901578 · Cited by 86
Cell-of-Origin DNA Methylation Signatures Are Maintained during Colorectal Carcinogenesis
Bormann, F., Rodríguez‐Paredes, M., Lasitschka, F., Edelmann, D., Musch, T., Benner, A., Bergman, Y., Dieter, S. M., Ball, C. R., Glimm, H., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.05.045 · Cited by 86
PRDM14: a unique regulator for pluripotency and epigenetic reprogramming
Nakaki, F., & Saitou, M. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.04.003 · Cited by 87
Prazeres, H., Torres, J., Rodrigues, F., Pinto, M. T., Pastoriza, M. C., Gomes, D., Cameselle‐Teijeiro, J., Vidal, A., Martins, T., Sobrinho-Simões, M. A., et al. (2016) · Oncogene · doi:10.1038/onc.2016.143 · Cited by 86
Melanoma epigenetics: novel mechanisms, markers, and medicines
Lee, J. J., Murphy, G. F., & Lian, C. G. (2014) · Laboratory Investigation · doi:10.1038/labinvest.2014.87 · Cited by 85
DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data
Gaspar, J. M., & Hart, R. P. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1909-0 · Cited by 85
Xu, X., Li, G., Li, C., Zhang, J., Wang, Q., Simmons, D. K., Chen, X., Wijesena, N. M., Zhu, W. Z., Wang, Z., et al. (2019) · National Science Review · doi:10.1093/nsr/nwz064 · Cited by 85
Epigenetic reprogramming of immune cells in injury, repair, and resolution
Placek, K., Schultze, J. L., & Aschenbrenner, A. C. (2019) · Journal of Clinical Investigation · doi:10.1172/jci124619 · Cited by 86
Barnett, K. R., Decato, B. E., Scott, T. J., Hansen, T. J., Chen, B., Attalla, J., Smith, A. D., & Hodges, E. C. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.01.004 · Cited by 85
Epigenetic effects of short-chain fatty acids from the large intestine on host cells
Stein, R. A., & Riber, L. (2023) · microLife · doi:10.1093/femsml/uqad032 · Cited by 85
Epigenomics of cancer – emerging new concepts
Hassler, M. R., & Egger, G. (2012) · Biochimie · doi:10.1016/j.biochi.2012.05.007 · Cited by 85
Liu, H., Liu, X., Zhang, S., Lv, J., Li, S., Shang, S., Jia, S., Wei, Y., Wang, F., Su, J., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1332 · Cited by 85
Epigenetics and Bone Remodeling
Husain, A., & Jeffries, M. A. (2017) · Current Osteoporosis Reports · doi:10.1007/s11914-017-0391-y · Cited by 85
DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes
Nothjunge, S., Nührenberg, T. G., Grüning, B. A., Doppler, S. A., Preißl, S., Schwaderer, M., Rommel, C., Krane, M., Hein, L., & Gilsbach, R. (2017) · Nature Communications · doi:10.1038/s41467-017-01724-9 · Cited by 85
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
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
Genetic and epigenetic instability in human pluripotent stem cells
Nguyen, H. T., Geens, M., & Spits, C. (2012) · Human Reproduction Update · doi:10.1093/humupd/dms048 · Cited by 84
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
Wang, Z., Wang, L., Zhang, Q., Tang, B., & Zhang, C. (2017) · Chemical Science · doi:10.1039/c7sc04813k · Cited by 84
Metadata
- Authors
- 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., Edsall, L., Antosiewicz-Bourget, J., Stewart, R., Ruotti, V., Millar, A. H., Thomson, J. A., Ren, B., & Ecker, J. R.
- Affiliations
- Salk Institute for Biological Studies (US)
- Ludwig Cancer Research (BE)
- Morgridge Institute for Research (US)
- The University of Western Australia (AU)
- University of Wisconsin–Madison (US)
- Corresponding author
- Ecker, Joseph R.
- ORCID
- Venue
- Nature
- Published
- 2009-10-14
- Volume
- 462
- Issue
- 7271
- Pages
- 315-322
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2857523
- OpenAlex
- W2059099579
- Cited by
- 4,673
- References
- 50
- Citations by year
- 2026: 132 · 2025: 178 · 2024: 214 · 2023: 207 · 2022: 237 · 2021: 251 · 2020: 232 · 2019: 256 · 2018: 273 · 2017: 282 · 2016: 304 · 2015: 356 · 2014: 350 · 2013: 374 · 2012: 373
- FWCI
- 136.77
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- UWA Profiles and Research Repository (UWA) (submittedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- BOA (University of Milano-Bicocca) (submittedVersion)
- Funders
- California Institute for Regenerative Medicine
- National Institutes of Health
- Australian Research Council (DP0771156, CE0561495)
- National Human Genome Research Institute (R01HG003523)
- National Institute of Environmental Health Sciences (U01ES017166, U01 1U01ES017166-01)
- 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 › Genetics › Genetic Syndromes and Imprinting
- Keywords
- DNA methylation, methylome, cytosine methylation, non-CG methylation, human embryonic stem cells, fetal fibroblasts, differentially methylated regions, pluripotency, cell differentiation, induced pluripotent stem cells, histone modifications, protein-DNA interactions, gene expression regulation, epigenome, gene body methylation, enhancer methylation
- MeSH terms
- Cell Line, DNA, DNA-Binding Proteins, Humans, Cluster Analysis, Genome, DNA Methylation, Epigenesis, Genetic, 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
