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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.
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“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]
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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
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ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads
Miller, C. A., Hampton, O. A., Coarfa, C., & Milosavljevic, A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016327 · Cited by 222
LncRNA-mediated DNA methylation: an emerging mechanism in cancer and beyond
Huang, W., Li, H., Yu, Q., Xiao, W., & Wang, D. O. (2022) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-022-02319-z · Cited by 222
Arechederra, M., Daian, F., Yim, A., Bazai, S. K., Richelme, S., Dono, R., Saurin, A. J., Habermann, B. H., & Maina, F. (2018) · Nature Communications · doi:10.1038/s41467-018-05550-5 · Cited by 221
Joint profiling of DNA methylation and chromatin architecture in single cells
Li, G., Liu, Y., Zhang, Y., Kubo, N., Yu, M., Fang, R., Kellis, M., & Ren, B. (2019) · Nature Methods · doi:10.1038/s41592-019-0502-z · Cited by 219
Self-citationFu, J., Wolfs, M. G. M., Deelen, P., Westra, H.-J., Fehrmann, R. S. N., Meerman, G. J. T., Buurman, W. A., Rensen, S. S., Groen, H. J. M., Weersma, R. K., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002431 · Cited by 218
MethylSig: a whole genome DNA methylation analysis pipeline
Park, Y., Figueroa, M. E., Rozek, L. S., & Sartor, M. A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu339 · Cited by 218
Allosteric control of mammalian DNA methyltransferases – a new regulatory paradigm
Jeltsch, A., & Jurkowska, R. Z. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw723 · Cited by 219
Intratumoral Heterogeneity of the Epigenome
Mazor, T., Pankov, A., Song, J. S., & Costello, J. (2016) · Cancer Cell · doi:10.1016/j.ccell.2016.03.009 · Cited by 217
Dynamic epigenomic landscapes during early lineage specification in mouse embryos
Zhang, Y., Xiang, Y., Yin, Q., Du, Z., Xu, P., Wang, Q., Fidalgo, M., Xia, W., Li, Y., Zhao, Z., et al. (2017) · Nature Genetics · doi:10.1038/s41588-017-0003-x · Cited by 217
Insights into epigenetic patterns in mammalian early embryos
Xu, R., Li, C., Liu, X., & Gao, S. (2021) · Protein & Cell · doi:10.1007/s13238-020-00757-z · Cited by 216
Insects as innovative models for functional studies of DNA methylation
Lyko, F., & Maleszka, R. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.01.003 · Cited by 215
The evidence for functional non-CpG methylation in mammalian cells
Patil, V., Ward, R. L., & Hesson, L. B. (2014) · Epigenetics · doi:10.4161/epi.28741 · Cited by 214
Nestor, C. E., Ruzov, A. S., Meehan, R. R., & Dunican, D. S. (2010) · BioTechniques · doi:10.2144/000113403 · Cited by 213
Evolutionary signals of selection on cognition from the great tit genome and methylome
Laine, V. N., Gossmann, T. I., Schachtschneider, K. M., Garroway, C. J., Madsen, O., Verhoeven, K. J. F., de Jager, V., Megens, H., Warren, W. C., Minx, P. J., et al. (2016) · Nature Communications · doi:10.1038/ncomms10474 · Cited by 213
Gao, L., Emperle, M., Guo, Y., Grimm, S. A., Ren, W., Adam, S., Uryu, H., Zhang, Z., Chen, D., Yin, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17109-4 · Cited by 213
A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
Feehery, G. R., Yigit, E., Oyola, S. O., Langhorst, B. W., Schmidt, V. T., Stewart, F. J., Dimalanta, E. T., Amaral-Zettler, L. A., Davis, T., Quail, M. A., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0076096 · Cited by 212
Genome-Wide Methylation Changes in the Brains of Suicide Completers
Labonté, B., Suderman, M., Maussion, G., Lopez, J. P., Navarro-Sánchez, L., Yerko, V., Mechawar, N., Szyf, M., Meaney, M. J., & Turecki, G. (2013) · American Journal of Psychiatry · doi:10.1176/appi.ajp.2012.12050627 · Cited by 212
Epigenetics and the regulation of stress vulnerability and resilience
Zannas, A. S., & West, A. E. (2014) · Neuroscience · doi:10.1016/j.neuroscience.2013.12.003 · Cited by 211
The Roles of Human DNA Methyltransferases and Their Isoforms in Shaping the Epigenome
Gujar, H., Weisenberger, D. J., & Liang, G. (2019) · Genes · doi:10.3390/genes10020172 · Cited by 210
Bainbridge, M. N., Wang, M., Wu, Y., Newsham, I., Muzny, D. M., Jefferies, J. L., Albert, T. J., Burgess, D. L., & Gibbs, R. A. (2011) · Genome biology · doi:10.1186/gb-2011-12-7-r68 · Cited by 208
Statham, A. L., Robinson, M. D., Song, J. Z., Coolen, M. W., Stirzaker, C., & Clark, S. J. (2012) · Genome Research · doi:10.1101/gr.132076.111 · Cited by 208
TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells
Verma, N., Pan, H., Doré, L. C., Shukla, A., Li, Q. V., Pelham‐Webb, B., Teijeiro, V., Gonzãlez, F., Krivtsov, A. V., Chang, C.-J., et al. (2017) · Nature Genetics · doi:10.1038/s41588-017-0002-y · Cited by 208
Single-Cell (Multi)omics Technologies
Chappell, L., Russell, A. J. C., & Voet, T. (2018) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091416-035324 · Cited by 207
Lynch, M., Smith, A. J. H., Gobbi, M. D., Flenley, M., Hughes, J. R., Vernimmen, D., Ayyub, H., Sharpe, J. A., Sloane-Stanley, J. A., Sutherland, L., et al. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.399 · Cited by 206
Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex
Zemach, A., & Zilberman, D. (2010) · Current Biology · doi:10.1016/j.cub.2010.07.007 · Cited by 206
Dynamics of DNA Methylation in Recent Human and Great Ape Evolution
Hernando-Herraez, I., Prado-Martinez, J., Garg, P., Fernández-Callejo, M., Heyn, H., Hvilsom, C., Navarro, A., Esteller, M., Sharp, A. J., & Marquès‐Bonet, T. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003763 · Cited by 206
Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution
Gao, L., Wu, K., Liu, Z., Yao, X., Yuan, S., Tao, W., Yi, L., Yu, G., Hou, Z., Fan, D., et al. (2018) · Cell · doi:10.1016/j.cell.2018.02.028 · Cited by 208
DNA methylation is required for the control of stem cell differentiation in the small intestinePreprint
Sheaffer, K. L., Kim, R., Aoki, R., Elliott, E. N., Schug, J., Burger, L., Schübeler, D., & Kaestner, K. H. (2014) · Genes & Development · doi:10.1101/gad.230318.113 · Cited by 206
Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors
Timp, W., Bravo, H. C., McDonald, O. G., Goggins, M., Umbricht, C. B., Zeiger, M. A., Feinberg, A. P., & Irizarry, R. A. (2014) · Genome Medicine · doi:10.1186/s13073-014-0061-y · Cited by 205
Ferry, L., Fournier, A., Tsusaka, T., Adelmant, G., Shimazu, T., Matano, S., Kirsh, O., Amouroux, R., Dohmae, N., Suzuki, T., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.07.012 · Cited by 203
Comparative Epigenomic Annotation of Regulatory DNA
Shu Dong, X. I. A. O., Xie, D., Cao, X., Yu, P., Xing, X., Chen, C.-C., Musselman, M., Xie, M., West, F. D., Lewin, H. A., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.029 · Cited by 203
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
TET proteins and 5‐methylcytosine oxidation in hematological cancers
Ko, M., An, J., Pastor, W. A., Koralov, S. B., Rajewsky, K., & Rao, A. (2014) · Immunological Reviews · doi:10.1111/imr.12239 · Cited by 202
Impaired DNA methylation and its mechanisms in CD4+T cells of systemic lupus erythematosus
Zhang, Y., Zhao, M., Sawalha, A. H., Richardson, B., & Lu, Q. (2013) · Journal of Autoimmunity · doi:10.1016/j.jaut.2013.01.005 · Cited by 202
Epigenetic mechanisms in diabetic vascular complications
Reddy, M. A., & Natarajan, R. D. (2011) · Cardiovascular Research · doi:10.1093/cvr/cvr024 · Cited by 202
Bocker, M., Hellwig, I., Breiling, A., Eckstein, V., Ho, A. D., & Lyko, F. (2011) · Blood · doi:10.1182/blood-2011-01-331926 · Cited by 201
Lou, S., Lee, H. M., Qin, H., Li, J., Gao, Z., Liu, X., Chan, L. L., Lam, V. K. L., So, W., Wang, Y., et al. (2014) · Genome biology · doi:10.1186/s13059-014-0408-0 · Cited by 203
Unique cell-type-specific patterns of DNA methylation in the root meristem
Kawakatsu, T., Stuart, T., Valdes, M., Breakfield, N. W., Schmitz, R. J., Nery, J. R., Urich, M. A., Han, X., Lister, R., Benfey, P. N., et al. (2016) · Nature Plants · doi:10.1038/nplants.2016.58 · Cited by 201
Self-citationDynamics 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
Stefanska, B., Karlic, H., Varga, F., Fabianowska‐Majewska, K., & Haslberger, A. (2012) · British Journal of Pharmacology · doi:10.1111/j.1476-5381.2012.02002.x · Cited by 200
Characterizing DNA methylation alterations from The Cancer Genome Atlas
Weisenberger, D. J. (2014) · Journal of Clinical Investigation · doi:10.1172/jci69740 · Cited by 200
Regional Activation of the Cancer Genome by Long-Range Epigenetic Remodeling
Bert, S. A., Robinson, M. D., Strbenac, D., Statham, A. L., Song, J. Z., Hulf, T., Sutherland, R. L., Coolen, M. W., Stirzaker, C., & Clark, S. J. (2012) · Cancer Cell · doi:10.1016/j.ccr.2012.11.006 · Cited by 200
Zhang, W., Spector, T. D., Deloukas, P., Bell, J. T., & Engelhardt, B. E. (2015) · Genome biology · doi:10.1186/s13059-015-0581-9 · Cited by 200
Durek, P., Nordström, K. J. V., Gasparoni, G., Salhab, A., Kressler, C., de Almeida, M., Bassler, K. E., Ulas, T., Schmidt, F., Xiong, J., et al. (2016) · Immunity · doi:10.1016/j.immuni.2016.10.022 · Cited by 200
Dayeh, T. A., Olsson, A. H., Volkov, P., Almgren, P., Rönn, T., & Ling, C. (2013) · Diabetologia · doi:10.1007/s00125-012-2815-7 · Cited by 199
Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers
Sérandour, A. A., Avner, S., Oger, F., Bizot, M., Percevault, F., Lucchetti-Miganeh, C., Palierne, G., Gheeraert, C., Barloy-Hubler, F., Péron, C. L., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks595 · Cited by 199
Ruike, Y., Imanaka, Y., Sato, F., Shimizu, K., & Tsujimoto, G. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-137 · Cited by 199
Saze, H., Tsugane, K., Kanno, T., & Nishimura, T. (2012) · Plant and Cell Physiology · doi:10.1093/pcp/pcs008 · Cited by 199
Feng, S. J., Liu, X. S., Tao, H., Tan, S. K., Chu, S. S., Oono, Y., Zhang, X. D., Chen, J., & Yang, Z. M. (2016) · Plant Cell & Environment · doi:10.1111/pce.12793 · Cited by 199
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
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Gutiérrez‐Arcelus, M., Ongen, H., Lappalainen, T., Montgomery, S. B., Buil, A., Yurovsky, A., Bryois, J., Padioleau, I., Romano, L., Planchon, A., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1004958 · Cited by 198
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Chedin, F. L. (2011) · Progress in molecular biology and translational science · doi:10.1016/b978-0-12-387685-0.00007-x · Cited by 196
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
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Miro-Blanch, J., & Yanes, O. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00638 · Cited by 195
Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi–Goutières syndrome
Lim, Y. W., Sanz, L. A., Xu, X., Hartono, S. R., & Chedin, F. L. (2015) · eLife · doi:10.7554/elife.08007 · Cited by 195
Whole genome DNA methylation analysis based on high throughput sequencing technology
Li, N., Ye, M., Li, Y., Yan, Z., Butcher, L. M., Sun, J., Han, X., Chen, Q., zhang, X., & Wang, J. (2010) · Methods · doi:10.1016/j.ymeth.2010.04.009 · Cited by 195
Potential in vivo roles of nucleic acid triple-helices
Buske, F. A., Mattick, J. S., & Bailey, T. L. (2011) · RNA Biology · doi:10.4161/rna.8.3.14999 · Cited by 195
Tagmentation-based whole-genome bisulfite sequencing
Wang, Q., Gu, L., Adey, A., Radlwimmer, B., Wang, W., Hovestadt, V., Bähr, M., Wolf, S., Shendure, J., Eils, R., et al. (2013) · Nature Protocols · doi:10.1038/nprot.2013.118 · Cited by 194
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Vats, S., Kumawat, S., Kumar, V., Patil, G., Joshi, T., Sonah, H., Sharma, T. R., & Deshmukh, R. K. (2019) · Cells · doi:10.3390/cells8111386 · Cited by 195
Liang, D., Zhang, Z., Wu, H., Huang, C., Shuai, P., Ye, C., Tang, S., Wang, Y., Yang, L., Wang, J., et al. (2014) · BMC Genetics · doi:10.1186/1471-2156-15-s1-s9 · Cited by 193
The NIH Roadmap Epigenomics Program data Resource
Chadwick, L. H. (2012) · Epigenomics · doi:10.2217/epi.12.18 · Cited by 193
Inferring regulatory element landscapes and transcription factor networks from cancer methylomes
Yao, L., Shen, H., Laird, P. W., Farnham, P., & Berman, B. P. (2015) · Genome biology · doi:10.1186/s13059-015-0668-3 · Cited by 193
DNA methylation of the oxytocin receptor gene predicts neural response to ambiguous social stimuli
Jack, A., Connelly, J. J., & Morris, J. P. (2012) · Frontiers in Human Neuroscience · doi:10.3389/fnhum.2012.00280 · Cited by 192
“, 2009)], and more recent evidence indicates its involvement in activation of transcription (Lister et al., 2009; as reviewed in Suzuki and Bird, 2008).”
BackgroundCandidate silencer elements for the human and mouse genomes
Jayavelu, N. D., Jajodia, A., Mishra, A., & Hawkins, R. D. (2020) · Nature Communications · doi:10.1038/s41467-020-14853-5 · Cited by 193
Self-citationTET 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
DNA methylation dynamics in aging: how far are we from understanding the mechanisms?
Ciccarone, F., Tagliatesta, S., Caiafa, P., & Zampieri, M. (2017) · Mechanisms of Ageing and Development · doi:10.1016/j.mad.2017.12.002 · Cited by 191
Soufi, A., & Dalton, S. (2016) · Development · doi:10.1242/dev.142075 · Cited by 190
Molecular Complexes at Euchromatin, Heterochromatin and Centromeric Chromatin
Morrison, O., & Thakur, J. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22136922 · Cited by 193
Robust single-cell DNA methylome profiling with snmC-seq2
Luo, C., Rivkin, A., Zhou, J., Sandoval, J. P., Kurihara, L., Lucero, J., Castanon, R., Nery, J. R., Pinto-Duarte, A., Bui, B., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06355-2 · Cited by 189
Self-citationZuo, X., Sheng, J., Lau, H.-T., McDonald, C. M., Andrade, M., Cullen, D. E., Bell, F. T., Iacovino, M., Kyba, M., Xu, G., et al. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.322644 · Cited by 189
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
Pflueger, C., Tan, D., Swain, T., Nguyen, T., Pflueger, J., Nefzger, C., Polo, J. M., Ford, E., & Lister, R. (2018) · Genome Research · doi:10.1101/gr.233049.117 · Cited by 188
Self-citationSegmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?
Nora, E. P., Dekker, J., & Heard, É. (2013) · BioEssays · doi:10.1002/bies.201300040 · Cited by 187
Olsson, A. H., Volkov, P., Bacos, K., Dayeh, T., Hall, E., Nilsson, E., Ladenvall, C., Rönn, T., & Ling, C. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004735 · Cited by 186
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Tsagaratou, A., Äijö, T., Lio, C. J., Yue, X., Huang, Y., Jacobsen, S. E., Lähdesmäki, H. J., & Rao, A. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1412327111 · Cited by 186
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Cooper, D. N., Chen, J., Ball, E. V., Howells, K., Mort, M. E., Phillips, A. D., Chuzhanova, N. A., Krawczak, M., Kehrer‐Sawatzki, H., & Stenson, P. D. (2010) · Human Mutation · doi:10.1002/humu.21260 · Cited by 186
SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas
Watanabe, H., Ma, Q., Peng, S., Adelmant, G., Swain, D., Song, W., Fox, C., Francis, J. M., Pedamallu, C. S., DeLuca, D. S., et al. (2014) · Journal of Clinical Investigation · doi:10.1172/jci71545 · Cited by 185
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Auclair, G., & Weber, M. (2012) · Biochimie · doi:10.1016/j.biochi.2012.05.016 · Cited by 185
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Yan, H., Bonasio, R., Simola, D. F., Liebig, J., Berger, S. L., & Reinberg, D. (2015) · Annual Review of Entomology · doi:10.1146/annurev-ento-010814-020803 · Cited by 183
Schreiber, J. M., Wescoe, Z. L., Abu-Shumays, R. L., Vivian, J., Baatar, B., Karplus, K. J., & Akeson, M. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1310615110 · Cited by 183
Castellano, S., Kuck, D., Viviano, M., Yoo, J., López-Vallejo, F., Conti, P., Tamborini, L., Pinto, A., Medina‐Franco, J. L., & Sbardella, G. (2011) · Journal of Medicinal Chemistry · doi:10.1021/jm2010404 · Cited by 183
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Kühnen, P., Mischke, M., Wiegand, S., Sers, C., Horsthemke, B., Lau, S., Keil, T. O. P., Lee, Y., Grueters, A., & Krude, H. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002543 · Cited by 182
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Xu, J., Watts, J. A., Pope, S. D., Gadue, P. J., Kamps, M. P., Plath, K., Zaret, K. S., & Smale, S. T. (2009) · Genes & Development · doi:10.1101/gad.1861209 · Cited by 182
Hemberger, M., Udayashankar, R., Tesar, P., Moore, H., & Burton, G. J. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq128 · Cited by 181
Brown, S. E., Teo, A. K. K., Pauklin, S., Hannan, N. R. F., Cho, C. H.-H., Lim, B., Vardy, L. A., Dunn, N. R., Trotter, M. W. B., Pedersen, R. A., et al. (2011) · Stem Cells · doi:10.1002/stem.666 · Cited by 181
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Angeloni, A., & Bogdanović, O. (2019) · Essays in Biochemistry · doi:10.1042/ebc20190030 · Cited by 181
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Dudley, K. J., Li, X., Kobor, M. S., Kippin, T. E., & Bredy, T. W. (2011) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2010.12.016 · Cited by 180
DNA methylation, a hand behind neurodegenerative diseases
Lu, H., Liu, X., Yu-Lin, D. E. N. G., & Qing, H. (2013) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2013.00085 · Cited by 181
Dolzhenko, E., & Smith, A. D. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-215 · Cited by 180
DNA methylation in human epigenomes depends on local topology of CpG sites
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Ginno, P. A., Gaidatzis, D., Feldmann, A., Hoerner, L., Imanci, D., Burger, L., Zilbermann, F., Peters, A. H. F. M., Edenhofer, F., Smallwood, S. A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16354-x · Cited by 179
Ruiz, S., Diep, D. H., Gore, A., Panopoulos, A. D., Montserrat, N., Plongthongkum, N., Kumar, S., Fung, H.-L., Giorgetti, A., Bilić, J., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1202352109 · Cited by 177
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Kuck, D., Singh, N. P., Lyko, F., & Medina‐Franco, J. L. (2009) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2009.11.050 · Cited by 175
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Sanchez-Mut, J. V., & Gräff, J. (2015) · Frontiers in Behavioral Neuroscience · doi:10.3389/fnbeh.2015.00347 · Cited by 175
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
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