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 301–400 of 1,010
The therapeutic potential of stem cells
Watt, F. M., & Driskell, R. R. (2009) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2009.0149 · Cited by 207
Zhang, B., Zhou, Y., Lin, N., Lowdon, R. F., Hong, C., Nagarajan, R. P., Cheng, J. B., Li, D., Stevens, M., Lee, H. J., et al. (2013) · Genome Research · doi:10.1101/gr.156539.113 · Cited by 199
Evolutionary conservation of the eumetazoan gene regulatory landscapePreprint
Schwaiger, M., Schönauer, A., Rendeiro, A. F., Pribitzer, C., Schauer, A., Gilles, A. F., Schinko, J. B., Renfer, E., Fredman, D., & Technau, U. (2014) · Genome Research · doi:10.1101/gr.162529.113 · Cited by 191
Taylor, G. C. A., Eskeland, R., Hekimoglu-Balkan, B., Pradeepa, M. M., & Bickmore, W. A. (2013) · Genome Research · doi:10.1101/gr.155028.113 · Cited by 203
Genome-wide screen of promoter methylation identifies novel markers in melanomaPreprint
Koga, Y., Pelizzola, M., Cheng, E., Krauthammer, M. O., Sznol, M., Ariyan, S., Narayan, D., Molinaro, A. M., Halaban, R., & Weissman, S. M. (2009) · Genome Research · doi:10.1101/gr.091447.109 · Cited by 197
Mining cancer methylomes: prospects and challenges
Stirzaker, C., Taberlay, P. C., Statham, A. L., & Clark, S. J. (2013) · Trends in Genetics · doi:10.1016/j.tig.2013.11.004 · Cited by 202
Wang, Y., Liu, H., & Sun, Z. S. (2017) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12322 · Cited by 200
Ishiyama, S., Nishiyama, A., Saeki, Y., Moritsugu, K., Morimoto, D., Yamaguchi, L., Arai, N., Matsumura, R., Kawakami, T., Mishima, Y., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.09.037 · Cited by 199
Alteration of Epigenetic Regulation by Long Noncoding RNAs in Cancer
Morlando, M., & Fatica, A. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19020570 · Cited by 197
What would you do if you could sequence everything?
Kahvejian, A., Quackenbush, J., & Thompson, J. F. (2008) · Nature Biotechnology · doi:10.1038/nbt1494 · Cited by 189
Martino, D., Loke, Y. J., Gordon, L., Ollikainen, M., Cruickshank, M. N., Saffery, R., & Craig, J. M. (2013) · Genome biology · doi:10.1186/gb-2013-14-5-r42 · Cited by 194
N-Myc–mediated epigenetic reprogramming drives lineage plasticity in advanced prostate cancer
Berger, A., Brady, N. J., Bareja, R., Robinson, B., Conteduca, V., Augello, M. A., Puca, L., Ahmed, A., Dardenne, É., Lü, X., et al. (2019) · Journal of Clinical Investigation · doi:10.1172/jci127961 · Cited by 195
Guo, H., Zhu, P., Guo, F., Li, X., Wu, X., Fan, X., Wen, L., & Tang, F. (2015) · Nature Protocols · doi:10.1038/nprot.2015.039 · Cited by 188
Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer
Kim, J. H., Dhanasekaran, S. M., Prensner, J. R., Cao, X., Robinson, D., Kalyana-Sundaram, S., Huang, C., Shankar, S., Jing, X., Iyer, M., et al. (2011) · Genome Research · doi:10.1101/gr.119347.110 · Cited by 188
Comprehensive analysis of long non-coding RNAs in human breast cancer clinical subtypes
Su, X., Malouf, G. G., Chen, Y., Zhang, J., Yao, H., Valero, V., Weinstein, J. N., Spano, J., Meric‐Bernstam, F., Khayat, D., et al. (2014) · Oncotarget · doi:10.18632/oncotarget.2454 · Cited by 186
TET family dioxygenases and DNA demethylation in stem cells and cancers
An, J., Rao, A., & Ko, M. (2017) · Experimental & Molecular Medicine · doi:10.1038/emm.2017.5 · Cited by 191
Neri, F., Křepelová, A., Incarnato, D., Maldotti, M., Parlato, C., Galvagni, F., Matarese, F., Stunnenberg, H. G., & Oliviero, S. (2013) · Cell · doi:10.1016/j.cell.2013.08.056 · Cited by 189
Dynamics and Context-Dependent Roles of DNA Methylation
Ambrosi, C. M., Manzo, M., & Baubec, T. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.02.008 · Cited by 201
Edwards, J. R., O’Donnell‐Luria, A., Rollins, R. A., Peckham, H. E., Lee, C. C., Milekic, M. H., Chanrion, B., Fu, Y., Su, T., Hibshoosh, H. H., et al. (2010) · Genome Research · doi:10.1101/gr.101535.109 · Cited by 196
Stem Cell Differentiation as a Non-Markov Stochastic Process
Stumpf, P. S., Smith, R. C. G., Lenz, M., Schuppert, A., Müller, F.-J., Babtie, A. C., Chan, T. E., Stumpf, M. P. H., Please, C. P., Howison, S., et al. (2017) · Cell Systems · doi:10.1016/j.cels.2017.08.009 · Cited by 190
Neri, F., Incarnato, D., Krepelova, A., Rapelli, S., Pagnani, A., Zecchina, R., Parlato, C., & Oliviero, S. (2013) · Genome Biology · doi:10.1186/gb-2013-14-8-r91 · Cited by 179
Evolution of the cancer genome
Podlaha, O., Riester, M., De, S., & Michor, F. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.01.003 · Cited by 188
DNA methylation and gene expression
Siegfried, Z., & Simon, I. (2009) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.64 · Cited by 186
Chromatin Regulatory Mechanisms in Pluripotency
Lessard, J. A., & Crabtree, G. R. (2010) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-051809-102012 · Cited by 185
Meyer, M. J., Fleming, J. M., Lin, A. F., Hussnain, S. A., Ginsburg, E., & Vonderhaar, B. K. (2010) · Cancer Research · doi:10.1158/0008-5472.can-09-3619 · Cited by 185
Sharma, M. D., Huang, L., Choi, J.-H., Lee, E.-J., Wilson, J. M., Lemos, H. D. P., Pan, F., Blazar, B. R., Pardoll, D. M., Mellor, A. L., et al. (2013) · Immunity · doi:10.1016/j.immuni.2013.01.013 · Cited by 180
Latest techniques to study DNA methylation
Gouil, Q. A., & Keniry, A. (2019) · Essays in Biochemistry · doi:10.1042/ebc20190027 · Cited by 187
Schellenberg, A., Lin, Q., Schüler, H. M., Koch, C., Joussen, S., Denecke, B., Walenda, G., Pallua, N., Suschek, C. V., Zenke, M., et al. (2011) · Aging · doi:10.18632/aging.100391 · Cited by 182
Seplyarskiy, V. B., Soldatov, R., Popadin, K. Y., Antonarakis, S. E., Bazykin, G. A., & Nikolaev, S. I. (2016) · Genome Research · doi:10.1101/gr.197046.115 · Cited by 175
Allele-specific DNA methylation: beyond imprinting
Tycko, B. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq376 · Cited by 179
Functional coupling between writers, erasers and readers of histone and DNA methylation
Torres, I. O., & Fujimori, D. G. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.09.007 · Cited by 185
DNA methylation in human epigenomes depends on local topology of CpG sites
Lövkvist, C., Dodd, I. B., Sneppen, K., & Haerter, J. O. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw124 · Cited by 180
Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
Pedersen, J. S., Valen, E., Velazquez, A. M. V., Parker, B. J., Rasmussen, M., Lindgreen, S., Lilje, B., Tobin, D. J., Kelly, T. K., Vang, S., et al. (2014) · Genome Research · doi:10.1101/gr.163592.113 · Cited by 170
Chávez, L., Józefczuk, J., Grimm, C., Dietrich, J., Timmermann, B., Lehrach, H., Herwig, R., & Adjaye, J. (2010) · Genome Research · doi:10.1101/gr.110114.110 · Cited by 171
The many faces of Pluripotency: in vitro adaptations of a continuum of in vivo states
Morgani, S. M., Nichols, J., & Hadjantonakis, A. (2017) · BMC Developmental Biology · doi:10.1186/s12861-017-0150-4 · Cited by 167
Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer
Risom, T., Langer, E. M., Chapman, M. P., Rantala, J., Fields, A. J., Boniface, C., Alvarez, M. J., Kendsersky, N. D., Pelz, C. R., Johnson-Camacho, K., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05729-w · Cited by 174
Fetal programming in meat production
Du, ., Wang, B., Fu, X., Yang, Q., & Zhu, M. J. (2015) · Meat Science · doi:10.1016/j.meatsci.2015.04.010 · Cited by 186
Identification of epigenetic DNA modifications with a protein nanopore
Wallace, E. V. B., Stoddart, D., Heron, A. J., Mikhailova, E., Maglia, G., Donohoe, T. J., & Bayley, H. (2010) · Chemical Communications · doi:10.1039/c0cc02864a · Cited by 176
Present and future challenges of induced pluripotent stem cells
Ohnuki, M., & Takahashi, K. (2015) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2014.0367 · Cited by 182
Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems
Nestor, C. E., Ottaviano, R., Reinhardt, D., Cruickshanks, H. A., Mjoseng, H. K., McPherson, R. C., Lentini, A., Thomson, J. P., Dunican, D. S., Pennings, S., et al. (2015) · Genome biology · doi:10.1186/s13059-014-0576-y · Cited by 178
Borengasser, S. J., Zhong, Y., Kang, P., Lindsey, F., Ronis, M. J. J., Badger, T. M., Gomez-Acevedo, H., & Shankar, K. (2013) · Endocrinology · doi:10.1210/en.2012-2255 · Cited by 172
Tissue-specific Distribution and Dynamic Changes of 5-Hydroxymethylcytosine in Mammalian Genomes
Kinney, S. R. M., Chin, H. G., Vaisvila, R., Bitinaite, J., Zheng, Y., Estève, P., Feng, S., Stroud, H., Jacobsen, S. E., & Pradhan, S. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.217083 · Cited by 172
Shaw, T., & Martin, P. (2009) · The EMBO Reports · doi:10.1038/embor.2009.102 · Cited by 171
Mechanisms of DNA methylation and demethylation in mammals
Auclair, G., & Weber, M. (2012) · Biochimie · doi:10.1016/j.biochi.2012.05.016 · Cited by 185
Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing
Horner, D. S., Pavesi, G., Castrignanò, T., Meo, P. D. D., Liuni, S., Sammeth, M., Picardi, E., & Pesole, G. (2009) · Briefings in Bioinformatics · doi:10.1093/bib/bbp046 · Cited by 183
Targeting epigenetics for cancer therapy
Park, J. W., & Han, J. (2019) · Archives of Pharmacal Research · doi:10.1007/s12272-019-01126-z · Cited by 171
Lu, L., Zhu, G., Zhang, C., Deng, Q., Katsaros, D., Mayne, S. T., Risch, H. A., Mu, L., Canuto, E. M., Gregori, G., et al. (2012) · Breast Cancer Research and Treatment · doi:10.1007/s10549-012-2314-z · Cited by 171
Genomic location analysis by ChIP‐Seq
Barski, A., & Zhao, K. (2009) · Journal of Cellular Biochemistry · doi:10.1002/jcb.22077 · Cited by 169
The RAG Recombinase Dictates Functional Heterogeneity and Cellular Fitness in Natural Killer Cells
Karo, J. M., Schatz, D. G., & Sun, J. C.-Y. (2014) · Cell · doi:10.1016/j.cell.2014.08.026 · Cited by 171
Redefining CpG islands using hidden Markov models
Wu, H., Caffo, B. S., Jaffee, H. A., Irizarry, R. A., & Feinberg, A. P. (2010) · Biostatistics · doi:10.1093/biostatistics/kxq005 · Cited by 167
Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter
Chen, H., Kazemier, H. G., de Groote, M. L., Ruiters, M. H. J., Xu, G., & Rots, M. G. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1019 · Cited by 164
Mulder, R. H., Neumann, A., Cecil, C. A. M., Walton, E., Houtepen, L. C., Simpkin, A. J., Rijlaarsdam, J., Heijmans, B. T., Gaunt, T. R., Felix, J. F., et al. (2021) · Human Molecular Genetics · doi:10.1093/hmg/ddaa280 · Cited by 165
Wan, J., Oliver, V. F., Wang, G., Zhu, H., Zack, D. J., Merbs, S. L., & Qian, J. (2015) · BMC Genomics · doi:10.1186/s12864-015-1271-4 · Cited by 165
Uniform, optimal signal processing of mapped deep-sequencing data
Kumar, V., Muratani, M., Rayan, N. A., Kraus, P., Lufkin, T., Ng, H., & Prabhakar, S. (2013) · Nature Biotechnology · doi:10.1038/nbt.2596 · Cited by 161
OSCA: a tool for omic-data-based complex trait analysis
Zhang, F., Chen, W., Zhu, Z., Zhang, Q., Nabais, M. F., Qi, T., Deary, I. J., Wray, N. R., Visscher, P. M., McRae, A. F., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1718-z · Cited by 147
Global DNA Demethylation During Mouse Erythropoiesis in Vivo
Shearstone, J. R., Pop, R., Bock, C., Boyle, P., Meissner, A., & Socolovsky, M. (2011) · Science · doi:10.1126/science.1207306 · Cited by 161
Self-citationDnmt3a -mutated clonal hematopoiesis promotes osteoporosis
Kim, P. G., Niroula, A., Shkolnik, V., McConkey, M., Lin, A. E., Słabicki, M., Kemp, J. P., Bick, A., Gibson, C. J., Griffin, G., et al. (2021) · Journal of Experimental Medicine · doi:10.1084/jem.20211872 · Cited by 164
Pancreatic neurogenin 3-expressing cells are unipotent islet precursors
Desgraz, R., & Herrera, P. L. (2009) · Development · doi:10.1242/dev.039214 · Cited by 170
Yagi, S., Hirabayashi, K., Sato, S., Li, W., Takahashi, Y., Hirakawa, T., Wu, G., Hattori, N., Hattori, N., Ohgane, J., et al. (2008) · Genome Research · doi:10.1101/gr.074070.107 · Cited by 162
Tumour Necrosis Factor Gene Polymorphism and Disease Prevalence
Qidwai, T., & Khan, F. (2011) · Scandinavian Journal of Immunology · doi:10.1111/j.1365-3083.2011.02602.x · Cited by 165
Zhang, Y., Rohde, C., Tierling, S., Jurkowski, T. P., Bock, C., Santacruz, D., Ragozin, S., Reinhardt, R., Groth, M., Walter, J., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000438 · Cited by 166
Chang, Y., Sun, L., Kokura, K., Horton, J. R., Fukuda, M., Espejo, A. B., Izumi, V., Koomen, J. M., Bedford, M. T., Zhang, X., et al. (2011) · Nature Communications · doi:10.1038/ncomms1549 · Cited by 163
Self-citationGenome-wide tracking of dCas9-methyltransferase footprints
Galonska, C., Charlton, J., Mattei, A. L., Donaghey, J., Clement, K., Gu, H., Mohammad, A. W., Stamenova, E. K., Cacchiarelli, D., Klages, S., et al. (2018) · Nature Communications · doi:10.1038/s41467-017-02708-5 · Cited by 160
Self-citationChen, H., Tian, Y., Shu, W., Bo, X., & Wang, S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0041374 · Cited by 161
DNA methylation based biomarkers: Practical considerations and applications
Kit, A. H., Nielsen, H. M., & Tost, J. (2012) · Biochimie · doi:10.1016/j.biochi.2012.07.014 · Cited by 163
Functions of DNA Methylation and Hydroxymethylation in Mammalian Development
Guibert, S., & Weber, M. (2013) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/b978-0-12-416027-9.00002-4 · Cited by 173
Arensbergen, J., García-Hurtado, J., Moran, I., Maestro, M. A., Xu, X., de Casteele, M. V., Skoudy, A. L., Palassini, M., Heimberg, H., & Ferrer, J. (2010) · Genome Research · doi:10.1101/gr.101709.109 · Cited by 167
Lowe, R., Gemma, C., Beyan, H., Hawa, M. I., Bazeos, A., Leslie, R. D., Montpetit, A., Rakyan, V. K., & Ramagopalan, S. V. (2013) · Epigenetics · doi:10.4161/epi.24362 · Cited by 160
Pioneer factors: directing transcriptional regulators within the chromatin environment
Magnani, L., Eeckhoute, J., & Lupien, M. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.07.002 · Cited by 173
DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells
Gu, T., Lin, X., Cullen, S. M., Luo, M., Jeong, M., Estecio, M. R., Shen, J., Hardikar, S., Sun, D., Su, J., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1464-7 · Cited by 163
DNA Hypomethylation and Hemimethylation in Cancer
Ehrlich, M., & Lacey, M. R. (2012) · Advances in experimental medicine and biology · doi:10.1007/978-1-4419-9967-2_2 · Cited by 163
Quenneville, S., Turelli, P., Bojkowska, K., Raclot, C., Offner, S., Kapopoulou, A., & Trono, D. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.08.043 · Cited by 160
Davison, J. M., Mellott, T. J., Kovacheva, V., & Blusztajn, J. K. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m807651200 · Cited by 158
Prediction of genome-wide DNA methylation in repetitive elements
Zheng, Y., Joyce, B. T., Liu, L., Zhang, Z., Kibbe, W. A., Zhang, W., & Hou, L. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx587 · Cited by 154
Stevens, M. W., Cheng, J. B., Li, D., Xie, M., Hong, C., Maire, C. L., Ligon, K. L., Hirst, M., Marra, M. A., Costello, J., et al. (2013) · Genome Research · doi:10.1101/gr.152231.112 · Cited by 160
Kozlenkov, A., Roussos, P., Timashpolsky, A., Barbu, M., Rudchenko, S., Bibikova, M. V., Klotzle, B., Byne, W. M., Lyddon, R., Narzo, A. F. D., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt838 · Cited by 159
Veland, N., Lu, Y., Hardikar, S., Gaddis, S., Zeng, Y., Liu, B., Estecio, M. R., Takata, Y., Lin, K., Tomida, M. W., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky947 · Cited by 150
Heyn, P. C., Logan, C. V., Fluteau, A., Challis, R. C., Auchynnikava, T., Martin, C.-A., Marsh, J. A., Taglini, F., Kilanowski, F. M., Parry, D. A., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0274-x · Cited by 160
Oda, M., Glass, J. L., Thompson, R. F., Mo, Y., Olivier, E. N., Figueroa, M. E., Selzer, R. R., Richmond, T., Zhang, X., Dannenberg, L. O., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp260 · Cited by 154
Self-citationDynamic DNA methylation: a prime candidate for genomic metaplasticity and behavioral adaptation
Baker‐Andresen, D., Ratnu, V. S., & Bredy, T. W. (2012) · Trends in Neurosciences · doi:10.1016/j.tins.2012.09.003 · Cited by 156
Developmental programming and epigenetics
Gabory, A., Attig, L., & Junien, C. (2011) · American Journal of Clinical Nutrition · doi:10.3945/ajcn.110.000927 · Cited by 164
Epigenetic control of gene expression: Potential implications for cancer treatment
Perri, F., Longo, F., Giuliano, M., Sabbatino, F., Favia, G., Ionna, F., Addeo, R., Scarpati, G. D. V., Lorenzo, G. D., & Pisconti, S. (2017) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2017.01.020 · Cited by 154
DNA methylation and its role in the pathogenesis of diabetes
Bansal, A., & Pinney, S. E. (2017) · Pediatric Diabetes · doi:10.1111/pedi.12521 · Cited by 166
Genome-Scale Dna Methylation Analysis
Fouse, S. D., Nagarajan, R. P., & Costello, J. (2010) · Epigenomics · doi:10.2217/epi.09.35 · Cited by 154
Wu, H., Wu, X., Shen, L., & Zhang, Y. (2014) · Nature Biotechnology · doi:10.1038/nbt.3073 · Cited by 157
Hackett, J. A., Reddington, J. P., Nestor, C. E., Dunican, D. S., Branco, M. R., Reichmann, J., Reik, W., Surani, M. A., Adams, I. R., & Meehan, R. R. (2012) · Development · doi:10.1242/dev.081661 · Cited by 157
Strogantsev, R., Krueger, F., Yamazawa, K., Shi, H., Gould, P., Goldman-Roberts, M., McEwen, K., Sun, B., Pedersen, R., & Ferguson-Smith, A. C. (2015) · Genome Biology · doi:10.1186/s13059-015-0672-7 · Cited by 152
Changes in correlation between promoter methylation and gene expression in cancer
Moarii, M., Boeva, V., Vert, J., & Reyal, F. (2015) · BMC Genomics · doi:10.1186/s12864-015-1994-2 · Cited by 156
Genome-wide loss of 5-hmC is a novel epigenetic feature of Huntington's disease
Wang, F., Yang, Y., Lin, X., Wang, J.-Q., Yong-sheng, W., Xie, W., Wang, D., Zhu, S., Liao, Y.-Q., Sun, Q., et al. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt214 · Cited by 155
Yang, Q.-Y., Liang, J.-F., Rogers, C. J., Zhao, J.-X., Zhu, M.-J., & Du, M. (2013) · Diabetes · doi:10.2337/db13-0433 · Cited by 152
Policarpi, C., Munafò, M., Tsagkris, S., Carlini, V., & Hackett, J. A. (2024) · Nature Genetics · doi:10.1038/s41588-024-01706-w · Cited by 163
Holstege, H., Pfeiffer, W., Sie, D., Hulsman, M., Nicholas, T. J., Lee, C. C., Ross, T., Lin, J., Miller, M. A., Ylstra, B., et al. (2014) · Genome Research · doi:10.1101/gr.162131.113 · Cited by 152
piRBase: a web resource assisting piRNA functional study
Zhang, P., Si, X., Skogerbø, G., Wang, J., Cui, D., Li, Y., Sun, X., Liu, L., Sun, B., Chen, R., et al. (2014) · Database · doi:10.1093/database/bau110 · Cited by 149
DNA methylation of cancer genome
Cheung, H., Lee, T., Rennert, O. M., & Chan, W. (2009) · Birth Defects Research Part C Embryo Today Reviews · doi:10.1002/bdrc.20163 · Cited by 153
An evaluation of methods correcting for cell-type heterogeneity in DNA methylation studies
McGregor, K., Bernatsky, S., Colmegna, I., Hudson, M., Pastinen, T., Labbe, A., & Greenwood, C. M. T. (2016) · Genome biology · doi:10.1186/s13059-016-0935-y · Cited by 148
A unique H3K4me2 profile marks tissue-specific gene regulationPreprint
Pękowska, A., Benoukraf, T., Ferrier, P., & Spicuglia, S. (2010) · Genome Research · doi:10.1101/gr.109389.110 · Cited by 157
Interplay Between Different Epigenetic Modifications and Mechanisms
Murr, R. (2010) · Advances in genetics · doi:10.1016/b978-0-12-380866-0.60005-8 · Cited by 154
Chromatin states in pluripotent, differentiated, and reprogrammed cells
Fisher, C. L., & Fisher, A. G. (2011) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2011.01.015 · Cited by 157
Understanding 'Non-genetic' Inheritance: Insights from Molecular-Evolutionary Crosstalk
Adrian‐Kalchhauser, I., Sultan, S. E., Shama, L. N. S., Spence-Jones, H. C., Tiso, S., Valsecchi, C. I. K., & Weissing, F. J. (2020) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2020.08.011 · Cited by 160
Oct transcription factors in development and stem cells: insights and mechanisms
Tantin, D. R. (2013) · Development · doi:10.1242/dev.095927 · Cited by 147
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
