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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Open accessAbstract
We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.
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“Useful tools will include maps of evolutionary conservation (108) and chromatin state (140), as well as databases of cell-state signatures, such as genome-wide expression patterns, that may integrate aspects of cell biology under resting and provoked conditions (141).”
From Genetic Mapping in Human Disease (2008) · cites this paper as [140]
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“Intriguingly, we also observed increased levels of both H3K18ac and H3K18cr at bivalent genes (Fig. 5B), that is, poised genes marked with both H3K4me3 and H3K27me3 in ES cells35,36, suggesting a role for HDAC1/2 in controlling the activity of developmentally regulated genes prior to ES cell differentiation.”
From Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo (2018) · cites this paper as [36]
In the citing paper
“Intriguingly, we also observed increased levels of both H3K18ac and H3K18cr at bivalent genes (Fig. 5B), that is, poised genes marked with both H3K4me3 and H3K27me3 in ES cells35,36, suggesting a role for HDAC1/2 in controlling the activity of developmentally regulated genes prior to ES cell differentiation.”
From Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo (2018) · cites this paper as [36]
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Cites
Chromatin modifications and their function
Kouzarides, T. (2007) · Cell · doi:10.1016/j.cell.2007.02.005 · Cited by 10,883
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-citationThe Role of Chromatin during Transcription
Li, B., Carey, M., & Workman, J. L. (2007) · Cell · doi:10.1016/j.cell.2007.01.015 · Cited by 3,503
The Transcriptional Landscape of the Mammalian Genome
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. A., et al. (2005) · Science · doi:10.1126/science.1112014 · Cited by 3,492
Polycomb complexes repress developmental regulators in murine embryonic stem cells
Boyer, L. A., Plath, K., Zeitlinger, J., Brambrink, T., Medeiros, L. A., Lee, T. I., Levine, S. S., Wernig, M., Tajonar, A., Ray, M. K., et al. (2006) · Nature · doi:10.1038/nature04733 · Cited by 2,568
Self-citationGenomic DNA methylation: the mark and its mediators.
Klose, R. J., & Bird, A. P. (2006) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2005.12.008 · Cited by 2,501
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
Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells
Lee, T. I., Jenner, R. G., Boyer, L. A., Guenther, M. G., Levine, S. S., Kumar, R., Chevalier, B. S., Johnstone, S. E., Cole, M. F., Isono, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.043 · Cited by 2,296
Self-citationBernstein, B. E., Meissner, A., & Lander, E. S. (2007) · Cell · doi:10.1016/j.cell.2007.01.033 · Cited by 2,086
Self-citationGeneration and initial analysis of more than 15,000 full-length human and mouse cDNA sequences
Mammalian Gene Collection (MGC) Program Team* (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.242603899 · Cited by 1,756
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Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
Self-citationHeinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682
Shrestha, S., & Offer, S. M. (2016) · Medical Epigenetics · doi:10.1159/000444713 · Cited by 8,951
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898
Self-citationIntegrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368
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Moore, L. D., Le, T., & Fan, G. (2013) · Neuropsychopharmacology · doi:10.1038/npp.2012.112 · Cited by 4,906
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Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., et al. (2009) · Nature · doi:10.1038/nature07672 · Cited by 4,098
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Rinn, J. L., & Chang, H. Y. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-051410-092902 · Cited by 4,091
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
Differential analysis of gene regulation at transcript resolution with RNA-seq
Trapnell, C., Hendrickson, D. G., Sauvageau, M., Goff, L., Rinn, J. L., & Pachter, L. (2013) · Nature Biotechnology · doi:10.1038/nbt.2450 · Cited by 3,492
The Polycomb complex PRC2 and its mark in life
Margueron, R., & Reinberg, D. (2011) · Nature · doi:10.1038/nature09784 · Cited by 3,347
Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes
Tsai, M.-C., Manor, O., Wan, Y., Mosammaparast, N., Wang, J. K., Lan, F., Shi, Y., Segal, E., & Chang, H. Y. (2010) · Science · doi:10.1126/science.1192002 · Cited by 3,290
CpG islands and the regulation of transcription
Deaton, A. M., & Bird, A. (2011) · Genes & Development · doi:10.1101/gad.2037511 · Cited by 3,187
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Mapping and analysis of chromatin state dynamics in nine human cell types
Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature · doi:10.1038/nature09906 · Cited by 2,898
Self-citationKhalil, A. M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B. E., van Oudenaarden, A., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904715106 · Cited by 2,872
Self-citationA decade of exploring the cancer epigenome—biological and translational implications
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RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M., & Gilad, Y. (2008) · Genome Research · doi:10.1101/gr.079558.108 · Cited by 2,771
Sharma, S., Kelly, T. K., & Jones, P. A. (2010) · Carcinogenesis · doi:10.1093/carcin/bgp220 · Cited by 2,637
Chen, X., Han, X., Yuan, P., Fang, F., Huss, M., Vega, V. B., Wong, E., Orlov, Y. L., Zhang, W., Jiang, J., et al. (2008) · Cell · doi:10.1016/j.cell.2008.04.043 · Cited by 2,547
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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Sachs, P., Ding, D., Bergmaier, P., Lamp, B., Schlagheck, C., Finkernagel, F., Nist, A., Stiewe, T., & Mermoud, J. E. (2019) · Nature Communications · doi:10.1038/s41467-019-09078-0 · Cited by 2,400
Single-cell chromatin accessibility reveals principles of regulatory variation
Buenrostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., Chang, H. Y., & Greenleaf, W. J. (2015) · Nature · doi:10.1038/nature14590 · Cited by 2,308
Modular regulatory principles of large non-coding RNAs
Guttman, M., & Rinn, J. L. (2012) · Nature · doi:10.1038/nature10887 · Cited by 2,298
Linking DNA methylation and histone modification: patterns and paradigms
Cedar, H., & Bergman, Y. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2540 · Cited by 2,267
Transcription factors: from enhancer binding to developmental control
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Huarte, M., Guttman, M., Feldser, D., Garber, M., Koziol, M. J., Kenzelmann-Broz, D., Khalil, A. M., Zuk, O., Amit, I., Rabani, M., et al. (2010) · Cell · doi:10.1016/j.cell.2010.06.040 · Cited by 2,053
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Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B. E., Bickel, P., Brown, J. B., Cayting, P., et al. (2012) · Genome Research · doi:10.1101/gr.136184.111 · Cited by 2,033
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Feng, J., Liu, T., Qin, B., Zhang, Y., & Liu, X. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.101 · Cited by 1,848
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Visel, A., Blow, M. J., Li, Z., Zhang, T., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F., et al. (2009) · Nature · doi:10.1038/nature07730 · Cited by 1,639
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Zaret, K. S., & Carroll, J. S. (2011) · Genes & Development · doi:10.1101/gad.176826.111 · Cited by 1,589
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Schones, D. E., Cui, K., Cuddapah, S., Roh, T., Barski, A., Wang, Z., Wei, G., & Zhao, K. (2008) · Cell · doi:10.1016/j.cell.2008.02.022 · Cited by 1,473
Kim, K. H., & Roberts, C. W. M. (2016) · Nature Medicine · doi:10.1038/nm.4036 · Cited by 1,471
Taverna, S. D., Li, H., Ruthenburg, A. J., Allis, C. D., & Patel, D. J. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1338 · Cited by 1,476
Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming
Jaenisch, R., & Young, R. A. (2008) · Cell · doi:10.1016/j.cell.2008.01.015 · Cited by 1,465
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Calo, E., & Wysocka, J. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.038 · Cited by 1,457
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Altshuler, D., Daly, M. J., & Lander, E. S. (2008) · Science · doi:10.1126/science.1156409 · Cited by 1,452
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Boyle, A. P., Davis, S., Shulha, H. P., Meltzer, P., Margulies, E. H., Weng, Z., Furey, T. S., & Crawford, G. E. (2008) · Cell · doi:10.1016/j.cell.2007.12.014 · Cited by 1,415
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Chen, C., Hu, Z., Liu, S., & Tseng, H. (2012) · Expert Opinion on Biological Therapy · doi:10.1517/14712598.2012.674507 · Cited by 1,413
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Black, J. C., Rechem, C. V., & Whetstine, J. R. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.11.006 · Cited by 1,391
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Goldberg, A. D., Banaszynski, L. A., Noh, K., Lewis, P. W., Elsässer, S. J., Stadler, S. C., Dewell, S. B., Law, M. J., Guo, X., Li, X., et al. (2010) · Cell · doi:10.1016/j.cell.2010.01.003 · Cited by 1,351
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Flavahan, W. A., Gaskell, E., & Bernstein, B. E. (2017) · Science · doi:10.1126/science.aal2380 · Cited by 1,340
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Rahl, P. B., Lin, C. Y., Seila, A. C., Flynn, R. A., McCuine, S., Burge, C. B., Sharp, P. A., & Young, R. A. (2010) · Cell · doi:10.1016/j.cell.2010.03.030 · Cited by 1,279
Guttman, M., Garber, M., Levin, J. Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M. J., Gnirke, A., Nusbaum, C., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1633 · Cited by 1,253
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Wei, G., Wei, L., Zhu, J., Zang, C., Hu-Li, J., Yao, Z., Cui, K., Kanno, Y., Roh, T.-Y., Watford, W. T., et al. (2009) · Immunity · doi:10.1016/j.immuni.2008.12.009 · Cited by 1,152
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Zhou, V. W., Goren, A., & Bernstein, B. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2905 · Cited by 1,147
Self-citationCovalent histone modifications — miswritten, misinterpreted and mis-erased in human cancers
Chi, P., Allis, C. D., & Wang, G. G. (2010) · Nature reviews. Cancer · doi:10.1038/nrc2876 · Cited by 1,131
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Gibney, E. R., & Nolan, C. M. (2010) · Heredity · doi:10.1038/hdy.2010.54 · Cited by 1,109
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Nie, Z., Hu, G., Wei, G., Cui, K., Yamane, A., Resch, W., Wang, R., Green, D. R., Tessarollo, L., Casellas, R. C., et al. (2012) · Cell · doi:10.1016/j.cell.2012.08.033 · Cited by 1,106
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Mercer, T. R., Dinger, M. E., Sunkin, S. M., Mehler, M. F., & Mattick, J. S. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706729105 · Cited by 1,103
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Laurent, L. C., Wong, E., Li, G., Huynh, T., Tsirigos, A., Ong, C. T., Low, H. M., Sung, K. W. K., Rigoutsos, I., Loring, J. F., et al. (2010) · Genome Research · doi:10.1101/gr.101907.109 · Cited by 1,082
Non‐coding RNAs: regulators of disease
Taft, R. J., Pang, K. C., Mercer, T. R., Dinger, M. E., & Mattick, J. S. (2009) · The Journal of Pathology · doi:10.1002/path.2638 · Cited by 1,080
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
Zang, C., Schones, D. E., Zeng, C., Cui, K., Zhao, K., & Peng, W. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp340 · Cited by 1,072
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Wu, H., & Zhang, Y. (2014) · Cell · doi:10.1016/j.cell.2013.12.019 · Cited by 1,065
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Ku, M., Koche, R. P., Rheinbay, E., Mendenhall, E. M., Endoh, M., Mikkelsen, T. S., Aiden, A. P., Nusbaum, C., Xie, X. S., Chi, A. S., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000242 · Cited by 1,053
Self-citationMolecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation
Peric-Hupkes, D., Meuleman, W., Pagie, L., Bruggeman, S. W. M., Solovei, I., Brugman, W., Gräf, S., Flicek, P., Kerkhoven, R. M., van Lohuizen, M., et al. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.03.016 · Cited by 1,050
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Lander, E. S. (2011) · Nature · doi:10.1038/nature09792 · Cited by 1,044
Self-citationMultivalent engagement of chromatin modifications by linked binding modules
Ruthenburg, A. J., Li, H., Patel, D. J., & Allis, C. D. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2298 · Cited by 1,039
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Williams, K., Christensen, J., Pedersen, M. T., Johansen, J. V., Cloos, P. A. C., Rappsilber, J., & Helin, K. (2011) · Nature · doi:10.1038/nature10066 · Cited by 1,021
Bossdorf, O., Richards, C. L., & Pigliucci, M. (2007) · Ecology Letters · doi:10.1111/j.1461-0248.2007.01130.x · Cited by 1,015
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Zhao, J. C., Ohsumi, T. K., Kung, J. T., Ogawa, Y., Grau, D., Sarma, K., Song, J. J., Kingston, R. E., Borowsky, M. L., & Lee, J. T. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.12.011 · Cited by 1,008
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Du, J., Johnson, L. M., Jacobsen, S. E., & Patel, D. J. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4043 · Cited by 1,000
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Loewer, S., Cabili, M. N., Guttman, M., Loh, Y., Thomas, K., Park, I. H., Garber, M. G., Curran, M. S., Önder, T. T., Agarwal, S., et al. (2010) · Nature Genetics · doi:10.1038/ng.710 · Cited by 988
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Lupien, M., Eeckhoute, J., Meyer, C. A., Wang, Q., Zhang, Y., Li, W., Carroll, J. S., Liu, X. S., & Brown, M. (2008) · Cell · doi:10.1016/j.cell.2008.01.018 · Cited by 983
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Li, H., Collado, M., Villasante, A., Strati, K., Ortega, S., Cañamero, M., Blasco, M. A., & Serrano, M. (2009) · Nature · doi:10.1038/nature08290 · Cited by 968
Mohn, F., Weber, M., Rebhan, M., Roloff, T. C., Richter, J., Stadler, M. B., Bibel, M., & Schübeler, D. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.05.007 · Cited by 970
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Suvà, M. L., Rheinbay, E., Gillespie, S. M., Patel, A. P., Wakimoto, H., Rabkin, S. D., Riggi, N., Chi, A. S., Cahill, D. P., Nahed, B. V., et al. (2014) · Cell · doi:10.1016/j.cell.2014.02.030 · Cited by 956
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Guo, H., Zhu, P., Yan, L., Li, R., Hu, B., Lian, Y., Yan, J., Ren, X., Lin, S., Li, J., et al. (2014) · Nature · doi:10.1038/nature13544 · Cited by 942
Illingworth, R. S., & Bird, A. P. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.04.012 · Cited by 940
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De Santa, F., Barozzi, I., Mietton, F., Ghisletti, S., Polletti, S., Tusi, B. K., Muller, H., Ragoussis, J., Wei, C.-L., & Natoli, G. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000384 · Cited by 934
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Seila, A. C., Calabrese, J. M., Levine, S. S., Yeo, G. W.-M., Rahl, P. B., Flynn, R. A., Young, R. A., & Sharp, P. A. (2008) · Science · doi:10.1126/science.1162253 · Cited by 930
Regulation of nucleosome dynamics by histone modifications
Zentner, G. E., & Henikoff, S. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2470 · Cited by 923
DNA methylation: a historical perspective
Mattei, A. L., Bailly, N., & Meissner, A. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.03.010 · Cited by 920
Self-citationCistrome Data Browser: expanded datasets and new tools for gene regulatory analysis
Zheng, R., Wan, C., Mei, S., Qin, Q., Wu, Q., Sun, H., Chen, C.-H., Brown, M. A., Zhang, X., Meyer, C. A., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1094 · Cited by 908
KAP1 controls endogenous retroviruses in embryonic stem cells
Rowe, H. M., Jakobsson, J., Mesnard, D., Rougemont, J., Reynard, S., Aktas, T., Maillard, P. V., Layard-Liesching, H., Verp, S., Marquis, J., et al. (2010) · Nature · doi:10.1038/nature08674 · Cited by 874
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A double take on bivalent promotersPreprint
Voigt, P., Tee, W., & Reinberg, D. (2013) · Genes & Development · doi:10.1101/gad.219626.113 · Cited by 863
Novel mutations target distinct subgroups of medulloblastoma
Robinson, G. W., Parker, M. D., Kranenburg, T. A., Lu, C., Chen, X. '., Ding, L., Phoenix, T. N., Hedlund, E., Wei, L., Zhu, X., et al. (2012) · Nature · doi:10.1038/nature11213 · Cited by 853
Deconstructing stem cell self-renewal: genetic insights into cell-cycle regulation
Orford, K. W., & Scadden, D. T. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2269 · Cited by 851
Yu, J., Yu, J., Mani, R.-S., Cao, Q., Brenner, C. J., Cao, X., Wang, X., Wu, L., Li, J., Hu, M., et al. (2010) · Cancer Cell · doi:10.1016/j.ccr.2010.03.018 · Cited by 850
Metadata
- Authors
- Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., Lee, W., Mendenhall, E., O’Donovan, A., Presser, A., Russ, C., Xie, X., Meissner, A., Wernig, M., Jaenisch, R., Nusbaum, C., Lander, E. S., & Bernstein, B. E.
- Affiliations
- Broad Institute (US)
- Children's Hospital (TN)
- Massachusetts General Hospital (US)
- Whitehead Institute for Biomedical Research (US)
- Corresponding author
- Lander, Eric S.
- Bernstein, Bradley E.
- ORCID
- Venue
- Nature
- Published
- 2007-07-01
- Volume
- 448
- Issue
- 7153
- Pages
- 553-560
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2921165
- OpenAlex
- W2017840637
- Cited by
- 4,129
- References
- 48
- Citations by year
- 2026: 58 · 2025: 78 · 2024: 106 · 2023: 116 · 2022: 144 · 2021: 200 · 2020: 127 · 2019: 185 · 2018: 163 · 2017: 200 · 2016: 210 · 2015: 277 · 2014: 291 · 2013: 340 · 2012: 364
- FWCI
- 122.52
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Open Access System for Information Sharing (Pohang University of Science and Technology) (submittedVersion)
- Funders
- National Cancer Institute (T32CA009216)
- National Institute of General Medical Sciences (R01GM078986)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- histone modifications, chromatin state, histone trimethylation, H3K4 trimethylation, H3K27me3, H3K36 trimethylation, H3K9 trimethylation, mouse embryonic stem cells, neural progenitor cells, embryonic fibroblasts, gene expression, gene repression, imprinting control regions, long terminal repeat, satellite DNA, telomeres, single nucleotide polymorphisms, ChIP-seq, pluripotency, lineage commitment
- MeSH terms
- Alleles, Animals, Chromatin, Fibroblasts, Histones, Male, Methylation, Promoter Regions, Genetic, Transcription, Genetic, Genome, Genomic Imprinting, Gene Expression Regulation, Developmental, CpG Islands, Cell Lineage, Pluripotent Stem Cells, Mice
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