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 601–700 of 1,035
Keller, T. E., Han, P., & Yi, S. V. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv345 · Cited by 148
DNA methylation at enhancers identifies distinct breast cancer lineages
Fleischer, T., Tekpli, X., Mathelier, A., Wang, S., Nebdal, D. J. H., Dhakal, H. P., Sahlberg, K. K., Schlichting, E., Sauer, T., Geisler, J., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00510-x · Cited by 148
A comparison of epigenetic mitotic-like clocks for cancer risk prediction
Teschendorff, A. E. (2020) · Genome Medicine · doi:10.1186/s13073-020-00752-3 · Cited by 148
DNA methylation and transcriptional noise
Huh, I., Zeng, J., Park, T., & Yi, S. V. (2013) · Epigenetics & Chromatin · doi:10.1186/1756-8935-6-9 · Cited by 147
DNA Methylation, Behavior and Early Life Adversity
Szyf, M. (2013) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2013.06.004 · Cited by 147
Whole genome DNA methylation: beyond genes silencing
Tirado-Magallanes, R., Rebbani, K., Lim, R., Pradhan, S., & Benoukraf, T. (2016) · Oncotarget · doi:10.18632/oncotarget.13562 · Cited by 147
Editing the Epigenome: Reshaping the Genomic Landscape
Holtzman, L., & Gersbach, C. A. (2018) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083117-021632 · Cited by 147
DNA methylation, early life environment, and health outcomes
Mitchell, C., Schneper, L. M., & Notterman, D. A. (2016) · Pediatric Research · doi:10.1038/pr.2015.193 · Cited by 146
Epigenetic control of gene regulation in plants
Lauria, M., & Rossi, V. (2011) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2011.03.002 · Cited by 146
Large-Scale Quality Analysis of Published ChIP-seq Data
Marinov, G. K., Kundaje, A. B., Park, P. J., & Wold, B. J. (2013) · G3 Genes Genomes Genetics · doi:10.1534/g3.113.008680 · Cited by 146
Cumulative Environmental Impacts: Science and Policy to Protect Communities
Solomon, G. M., Morello-Frosch, R. A., Zeise, L. A., & Faust, J. B. (2015) · Annual Review of Public Health · doi:10.1146/annurev-publhealth-032315-021807 · Cited by 146
Interplay between chromatin marks in development and disease
Janssen, S. M., & Lorincz, M. C. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00416-x · Cited by 147
Kubo, N., Toh, H., Shirane, K., Shirakawa, T., Kobayashi, H., Sato, T., Sone, H., Sato, Y., Tomizawa, S.-I., Tsurusaki, Y., et al. (2015) · BMC Genomics · doi:10.1186/s12864-015-1833-5 · Cited by 145
Wang, X., Li, Q., Lian, J., Li, L., Jin, L., Cai, H., Xu, F., Qi, H., Zhang, L., Wu, F., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-1119 · Cited by 145
Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome
Inagaki, S., Miura-Kamio, A., Nakamura, Y., Lu, F., Cui, X., Cao, X., Kimura, H., Saze, H., & Kakutani, T. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.227 · Cited by 145
Primate CpG Islands Are Maintained by Heterogeneous Evolutionary Regimes Involving Minimal Selection
Cohen, N. M., Kenigsberg, E., & Tanay, A. (2011) · Cell · doi:10.1016/j.cell.2011.04.024 · Cited by 145
Epigenetic Underpinnings of Developmental Sex Differences in the Brain
Nugent, B. M., & McCarthy, M. M. (2011) · Neuroendocrinology · doi:10.1159/000325264 · Cited by 145
Rondelet, G., Maso, T. D., Willems, L., & Wouters, J. (2016) · Journal of Structural Biology · doi:10.1016/j.jsb.2016.03.013 · Cited by 145
Sun, Y. V., Smith, A. K., Conneely, K. N., Chang, Q., Li, W., Zagel, A. L., Smith, J. A., Almli, L. M., Binder, E. B., Klengel, T., et al. (2013) · Human Genetics · doi:10.1007/s00439-013-1311-6 · Cited by 144
Epigenetics in breast cancer: what's new?
Huang, Y., Nayak, S. R., Jankowitz, R. C., Davidson, N. E., & Oesterreich, S. (2011) · Breast Cancer Research · doi:10.1186/bcr2925 · Cited by 144
TET Enzymes and 5hmC in Adaptive and Innate Immune Systems
Lio, C. J., & Rao, A. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.00210 · Cited by 144
Epigenetic Regulations in Neuropsychiatric Disorders
Kuehner, J. N., Bruggeman, E. C., Wen, Z., & Yao, B. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00268 · Cited by 144
Pham, T.-H., Benner, C., Lichtinger, M., Schwarzfischer, L., Hu, Y., Andreesen, R., Chen, W., & Rehli, M. (2012) · Blood · doi:10.1182/blood-2012-01-402453 · Cited by 143
Epigenetic flexibility in metabolic regulation: disease cause and prevention
Kirchner, H., Osler, M. E., Krook, A., & Zierath, J. R. (2013) · Trends in Cell Biology · doi:10.1016/j.tcb.2012.11.008 · Cited by 143
The role of methylation of DNA in environmental adaptation
Flores, K. B., Wolschin, F., & Amdam, G. V. (2013) · Integrative and Comparative Biology · doi:10.1093/icb/ict019 · Cited by 143
Identification of Driver and Passenger DNA Methylation in Cancer by Epigenomic Analysis
Kalari, S. K., & Pfeifer, G. P. (2010) · Advances in genetics · doi:10.1016/b978-0-12-380866-0.60010-1 · Cited by 143
Mammalian epigenetic mechanisms
Zhang, G., & Pradhan, S. (2014) · IUBMB Life · doi:10.1002/iub.1264 · Cited by 143
A comprehensive epigenome atlas reveals DNA methylation regulating skeletal muscle development
Yang, Y., Fan, X., Yan, J., Chen, M., Zhu, M., Tang, Y., Liu, S., & Tang, Z. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1203 · Cited by 146
The impact of epigenetics on cardiovascular disease
Prasher, D., Greenway, S. C., & Singh, R. B. (2019) · Biochemistry and Cell Biology · doi:10.1139/bcb-2019-0045 · Cited by 143
Accelerated Placental Aging in Early Onset Preeclampsia Pregnancies Identified By DNA Methylation
Mayne, B. T., Leemaqz, S., Smith, A. K., Breen, J., Roberts, C. T., & Bianco‐Miotto, T. (2016) · Epigenomics · doi:10.2217/epi-2016-0103 · Cited by 141
Dynamic DNA methylation during aging: A "prophet" of age-related outcomes
Xiao, F.-H., Wang, H.-T., & Kong, Q.-P. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00107 · Cited by 140
Liang, P., Song, F., Ghosh, S., Morien, E., Qin, M., Mahmood, S., Fujiwara, K., Igarashi, J., Nagase, H., & Held, W. A. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-231 · Cited by 140
Genome-wide detection of cytosine methylation by single molecule real-time sequencing
Tse, O. Y. O., Jiang, P., Cheng, S. H., Peng, W., Shang, H., Wong, J., Chan, S. L., Poon, L. C., Leung, T. Y., Chan, K. C. A., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2019768118 · Cited by 140
Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation
Hughes, A. L., Kelley, J. R., & Klose, R. J. (2020) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2020.194567 · Cited by 139
The H3K4-Methyl Epigenome Regulates Leukemia Stem Cell Oncogenic Potential
Wong, S. H. K., Goode, D. L., 岩崎, 正., Wei, M. C., Kuo, H.-P., Zhu, L., Schneidawind, D., Duque‐Afonso, J., Weng, Z., & Cleary, M. L. (2015) · Cancer Cell · doi:10.1016/j.ccell.2015.06.003 · Cited by 139
Epigenomics and Interindividual Differences in Drug Response
Ivanov, M., Kacevska, M., & Ingelman‐Sundberg, M. (2012) · Clinical Pharmacology & Therapeutics · doi:10.1038/clpt.2012.152 · Cited by 139
DNA Methylation and Susceptibility to Autism Spectrum Disorder
Tremblay, M. W., & Jiang, Y. (2019) · Annual Review of Medicine · doi:10.1146/annurev-med-120417-091431 · Cited by 139
Small extracellular vesicles in cancer
Abhange, K. K., Makler, A., Wen, Y., Ramnauth, N., Mao, W., Asghar, W., & Wan, Y. (2021) · Bioactive Materials · doi:10.1016/j.bioactmat.2021.03.015 · Cited by 139
Wienholz, B. L., Kareta, M. S., Moarefi, A. H., Gordon, C. A., Ginno, P. A., & Chedin, F. L. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001106 · Cited by 139
Butcher, L. M., & Beck, S. (2014) · Methods · doi:10.1016/j.ymeth.2014.10.036 · Cited by 138
On how mammalian transcription factors recognize methylated DNA
Buck‐Koehntop, B. A., & Defossez, P. (2013) · Epigenetics · doi:10.4161/epi.23632 · Cited by 138
Chromatin deregulation in disease
Mirabella, A., Foster, B. M., & Bartke, T. (2015) · Chromosoma · doi:10.1007/s00412-015-0530-0 · Cited by 139
Epigenetic Biomarkers in Cell-Free DNA and Applications in Liquid Biopsy
Gai, W., & Sun, K. (2019) · Genes · doi:10.3390/genes10010032 · Cited by 138
DNA methylation in thyroid cancer
Zafón, C., Gil, J., Pérez-González, B., & Jordà, M. (2019) · Endocrine Related Cancer · doi:10.1530/erc-19-0093 · Cited by 138
Environmental exposures influence multigenerational epigenetic transmission
Klibaner-Schiff, E., Simonin, E. M., Akdiş, C. A., Cheong, A. W. Y., Johnson, M. M. D., Karagas, M. R., Kirsh, S., Kline, O., Mazumdar, M., Oken, E., et al. (2024) · Clinical Epigenetics · doi:10.1186/s13148-024-01762-3 · Cited by 138
Rogler (2015) · doi:10.1097/mib.0000000000000229 · Cited by 137
Chromatin density and splicing destiny: on the cross‐talk between chromatin structure and splicing
Schwartz, S., & Ast, G. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.71 · Cited by 137
Eating disorders, gene–environment interactions and epigenetics
Campbell, I. C., Mill, J. S., Uher, R., & Schmidt, U. H. (2010) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2010.09.012 · Cited by 136
Deletion of the de novo DNA methyltransferase Dnmt3a promotes lung tumor progression
Gao, Q., Steine, E. J., Barrasa, M. I., Hockemeyer, D. F., Pawlak, M., Fu, D., Reddy, S., Bell, G. W., & Jaenisch, R. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1114946108 · Cited by 136
The epigenome as a therapeutic target in prostate cancer
Perry, A. S., Watson, R. W. G., Lawler, M., & Hollywood, D. P. (2010) · Nature Reviews Urology · doi:10.1038/nrurol.2010.185 · Cited by 136
Epigenetics and Cardiovascular Disease
Webster, A., Yan, M. S.-C., & Marsden, P. A. (2012) · Canadian Journal of Cardiology · doi:10.1016/j.cjca.2012.10.023 · Cited by 136
Günther, K., Rust, M., Leers, J., Boettger, T., Scharfe, M., Jarek, M., Bartkuhn, M., & Renkawitz, R. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt035 · Cited by 136
Cooper, D. N., Bacolla, A., Férec, C., Vásquez, K. M., Kehrer‐Sawatzki, H., & Chen, J. (2011) · Human Mutation · doi:10.1002/humu.21557 · Cited by 136
Zheng, X., Zhang, N., Wu, H., & Wu, H. (2017) · Genome biology · doi:10.1186/s13059-016-1143-5 · Cited by 136
Maenohara, S., Unoki, M., Toh, H., Ohishi, H., Sharif, J., Koseki, H., & Sasaki, H. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1007042 · Cited by 136
Hypomethylation of Repeated Dna Sequences in Cancer
Ross, J. P., Rand, K. N., & Molloy, P. L. (2010) · Epigenomics · doi:10.2217/epi.10.2 · Cited by 136
DNA methylation and epigenetic control of cellular differentiation
Khavari, D. A., Sen, G. L., & Rinn, J. L. (2010) · Cell Cycle · doi:10.4161/cc.9.19.13385 · Cited by 135
DNA Methylation: A Timeline of Methods and Applications
Harrison, A. J., & Parle‐McDermott, A. (2011) · Frontiers in Genetics · doi:10.3389/fgene.2011.00074 · Cited by 135
Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved
Long, H. K., King, H. W., Patient, R. K., Odom, D. T., & Klose, R. J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw258 · Cited by 135
Tissue-specific 5-hydroxymethylcytosine landscape of the human genome
He, B., Zhang, C., Zhang, X., Fan, Y., Zeng, H., Liu, J., Meng, H., Bai, D., Peng, J., Zhang, Q., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24425-w · Cited by 135
Schrey, A. W., Coon, C. A. C., Grispo, M. T., Awad, M., Imboma, T. S., McCoy, E. D., Mushinsky, H. R., Richards, C. L., & Martin, L. B. (2012) · Genetics Research International · doi:10.1155/2012/979751 · Cited by 134
Minireview: Epigenetics of Obesity and Diabetes in Humans
Slomko, H., Heo, H. J., & Einstein, F. H. (2012) · Endocrinology · doi:10.1210/en.2011-1759 · Cited by 134
Lee, W., Johnson, J., Gough, D. J., Donoghue, J. F., Cagnone, G., Vaghjiani, V., Brown, K. A., Johns, T. G., & John, J. C. S. (2015) · Cell Death and Disease · doi:10.1038/cddis.2015.34 · Cited by 133
Epigenetic regulation in pluripotent stem cells: a key to breaking the epigenetic barrier
Watanabe, A., Yamada, Y., & Yamanaka, S. (2012) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2012.0292 · Cited by 133
DNA methylation signatures for breast cancer classification and prognosis
Szyf, M. (2012) · Genome Medicine · doi:10.1186/gm325 · Cited by 133
Allele-specific methylation in the human genome: Implications for genetic studies of complex disease
Meaburn, E. L., Schalkwyk, L. C., & Mill, J. (2010) · Epigenetics · doi:10.4161/epi.5.7.12960 · Cited by 132
Wu, H., & Zhang, Y. (2011) · Cell Cycle · doi:10.4161/cc.10.15.16930 · Cited by 132
Strategies for discovery and validation of methylated and hydroxymethylated DNA biomarkers
Olkhov‐Mitsel, E., & Bapat, B. V. (2012) · Cancer Medicine · doi:10.1002/cam4.22 · Cited by 132
Chromatin plasticity and genome organization in pluripotent embryonic stem cells
Mattout, A., & Meshorer, E. (2010) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2010.02.001 · Cited by 132
Zhang, Y., Maksimovic, J., Naselli, G., Qian, J., Chopin, M., Blewitt, M. E., Oshlack, A., & Harrison, L. C. (2013) · Blood · doi:10.1182/blood-2013-02-481788 · Cited by 132
The quantitative proteomes of human‐induced pluripotent stem cells and embryonic stem cells
Muñoz, J., Low, T. Y., Kok, Y. J., Chin, A. C. P., Frese, C. K., Ding, V., Choo, A. B. H., & Heck, A. J. R. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.84 · Cited by 132
DNA methylation and application in forensic sciences
Kader, F., & Ghai, M. (2015) · Forensic Science International · doi:10.1016/j.forsciint.2015.01.037 · Cited by 132
Cytidine deaminases: AIDing DNA demethylation?Preprint
Fritz, E. L., & Papavasiliou, F. N. (2010) · Genes & Development · doi:10.1101/gad.1963010 · Cited by 132
Active DNA Demethylation in Plants and AnimalsPreprint
Zhang, H., & Zhu, J. (2012) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2012.77.014936 · Cited by 132
A comparison of gene expression and DNA methylation patterns across tissues and speciesPreprint
Blake, L. E., Roux, J., Hernando-Herraez, I., Banovich, N. E., García-Pérez, R., Hsiao, C. J., Eres, I. E., Chavarria, C., Marquès‐Bonet, T., & Gilad, Y. (2020) · Genome Research · doi:10.1101/gr.254904.119 · Cited by 132
DNA methylation changes induced by long and short photoperiods inNasoniaPreprint
Pegoraro, M., Bafna, A., Davies, N. J., Shuker, D. M., & Tauber, E. (2015) · Genome Research · doi:10.1101/gr.196204.115 · Cited by 132
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing
Lutsik, P., Feuerbach, L., Arand, J., Lengauer, T., Walter, J., & Bock, C. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr312 · Cited by 131
The mutational landscape of chromatin regulatory factors across 4,623 tumor samples
González-Pérez, A., Jené-Sanz, A., & López-Bigas, N. (2013) · Genome biology · doi:10.1186/gb-2013-14-9-r106 · Cited by 131
The chemistries and consequences of DNA and RNA methylation and demethylation
Traube, F. R., & Carell, T. (2017) · RNA Biology · doi:10.1080/15476286.2017.1318241 · Cited by 131
High-resolution characterization of sequence signatures due to non-random cleavage of cell-free DNA
Chandrananda, D., Thorne, N., & Bahlo, M. (2015) · BMC Medical Genomics · doi:10.1186/s12920-015-0107-z · Cited by 130
The emerging role of epigenetics in cardiovascular disease
Khalil, C. A. (2014) · Therapeutic Advances in Chronic Disease · doi:10.1177/2040622314529325 · Cited by 130
Contrasting chromatin organization of CpG islands and exons in the human genome
Choi, J. K. (2010) · Genome biology · doi:10.1186/gb-2010-11-7-r70 · Cited by 130
Epigenetic control of gene regulation during development and disease: A view from the retina
Corso‐Díaz, X., Jaeger, C., Chaitankar, V., & Swaroop, A. (2018) · Progress in Retinal and Eye Research · doi:10.1016/j.preteyeres.2018.03.002 · Cited by 130
A Practical Guide to the Measurement and Analysis of DNA Methylation
Singer, B. D. (2019) · American Journal of Respiratory Cell and Molecular Biology · doi:10.1165/rcmb.2019-0150tr · Cited by 130
de Mendoza, A., Nguyen, T. V., Ford, E., Poppe, D., Buckberry, S., Pflueger, J., Grimmer, M., Stolzenburg, S., Bogdanović, O., Oshlack, A., et al. (2022) · Genome biology · doi:10.1186/s13059-022-02728-5 · Cited by 130
Self-citationAn Epigenetic Role of Mitochondria in Cancer
Liu, Y., Chen, C., Wang, X., Sun, Y., Zhang, J., Chen, J., & Shi, Y. (2022) · Cells · doi:10.3390/cells11162518 · Cited by 131
The MspJI family of modification-dependent restriction endonucleases for epigenetic studies
Cohen-Karni, D., Xu, D., Apone, L., Fomenkov, A. I., Sun, Z., Davis, P. J., Kinney, S. R. M., Mabuchi, M. Y., Xu, S.-Y., Davis, T. B., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1018448108 · Cited by 130
Yan, H., Kikuchi, S., Neumann, P., Zhang, W., Wu, Y., Chen, F., & Jiang, J. (2010) · The Plant Journal · doi:10.1111/j.1365-313x.2010.04246.x · Cited by 130
Zhang, Z., Chung, S., Xu, Z. Q., & Xu, Y. (2013) · Stem Cells · doi:10.1002/stem.1532 · Cited by 129
QDMR: a quantitative method for identification of differentially methylated regions by entropy
Zhang, Y., Liu, H., Lv, J., Xiao, X., Zhu, J., Liu, X., Su, J., Li, X., Wu, Q., Wang, F., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr053 · Cited by 129
Substantial DNA methylation differences between two major neuronal subtypes in human brain
Kozlenkov, A., Wang, M., Roussos, P., Rudchenko, S., Barbu, M., Bibikova, M. V., Klotzle, B., Dwork, A. J., Zhang, B., Hurd, Y. L., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1304 · Cited by 130
Homeobox oncogene activation by pan-cancer DNA hypermethylation
Su, J., Huang, Y., Cui, X., Wang, X., Zhang, X., Lei, Y., Xu, J., Lin, X., Chen, K., Lv, J., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1492-3 · Cited by 130
Stress and the epigenetic landscape: a link to the pathobiology of human diseases?
Johnstone, S. E., & Baylin, S. B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2881 · Cited by 131
DNA methylation: Insights into human evolution
Hernando-Herraez, I., Garcia-Perez, R., Sharp, A. J., & Marques-Bonet, T. (2015) · PLOS Genetics · doi:10.1371/journal.pgen.1005661 · Cited by 128
A “mille-feuille” of silencing: Epigenetic control of transposable elements
Rigal, M., & Mathieu, O. (2011) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2011.04.001 · Cited by 128
Statistical methods for detecting differentially methylated loci and regions
Robinson, M. D., Kahraman, A., Law, C. W., Lindsay, H. A., Nowicka, M., Weber, L. M., & Zhou, X. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00324 · Cited by 128
Isoform‐specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands
Manzo, M., Wirz, J., Ambrosi, C. M., Villaseñor, R., Roschitzki, B., & Baubec, T. (2017) · The EMBO Journal · doi:10.15252/embj.201797038 · Cited by 128
Histone acetylation recruits the SWR1 complex to regulate active DNA demethylation in Arabidopsis
Nie, W., Lei, M., Zhang, M., Tang, K., Huang, H., Zhang, C., Miki, D., Liu, P., Yang, Y., Wang, X., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1906023116 · Cited by 128
Hamamoto, R., Komatsu, M., Takasawa, K., Asada, K., & Kaneko, S. (2019) · Biomolecules · doi:10.3390/biom10010062 · Cited by 128
Ultra-low-input, tagmentation-based whole-genome bisulfite sequencingPreprint
Adey, A., & Shendure, J. (2012) · Genome Research · doi:10.1101/gr.136242.111 · Cited by 128
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
