Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

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

The 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

Genomic 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

Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome

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

The Mammalian Epigenome

Bernstein, B. E., Meissner, A., & Lander, E. S. (2007) · Cell · doi:10.1016/j.cell.2007.01.033 · Cited by 2,086

Generation 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

Phosphorylation of EZH2 Activates STAT3 Signaling via STAT3 Methylation and Promotes Tumorigenicity of Glioblastoma Stem-like Cells

Kim, E. H., Kim, M., Woo, D., Shin, Y., Shin, J., Chang, N., Oh, Y. T., Kim, H., Rheey, J., Nakano, I., et al. (2013) · Cancer Cell · doi:10.1016/j.ccr.2013.04.008 · Cited by 846

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

Matsui, T., Leung, D., Miyashita, H., Maksakova, I. A., Miyachi, H., Kimurâ, H., Tachibana, M., Lorincz, M. C., & Shinkai, Y. (2010) · Nature · doi:10.1038/nature08858 · Cited by 842

ALLPATHS: De novo assembly of whole-genome shotgun microreadsPreprint

Butler, J., MacCallum, I., Kleber, M., Shlyakhter, I. A., Belmonte, M. K., Lander, E. S., Nusbaum, C., & Jaffe, D. B. (2008) · Genome Research · doi:10.1101/gr.7337908 · Cited by 823

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

Ramsköld, D., Wang, E. T., Burge, C. B., & Sandberg, R. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000598 · Cited by 820

Defining cell types and states with single-cell genomics

Trapnell, C. (2015) · Genome Research · doi:10.1101/gr.190595.115 · Cited by 813

Histone modification levels are predictive for gene expression

Karlić, R., Chung, H., Lasserre, J., Vlahoviček, K., & Vingron, M. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909344107 · Cited by 809

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

Pastor, W. A., Pape, U. J., Huang, Y., Henderson, H. R., Lister, R., Ko, M., McLoughlin, E. M., Brudno, Y., Mahapatra, S., Kapranov, P., et al. (2011) · Nature · doi:10.1038/nature10102 · Cited by 804

Variant PRC1 Complex-Dependent H2A Ubiquitylation Drives PRC2 Recruitment and Polycomb Domain Formation

Blackledge, N. P., Farcas, A. M., Kondo, T., King, H. W., McGouran, J. F., Hanssen, L. L. P., Ito, S., Cooper, S., Kondo, K., Koseki, Y., et al. (2014) · Cell · doi:10.1016/j.cell.2014.05.004 · Cited by 778

Chromatin state dynamics during blood formation

Lara-Astiaso, D., Weiner, A., Lorenzo-Vivas, E., Zaretsky, I., Jaitin, D. A., David, E., Keren-Shaul, H., Mildner, A., Winter, D., Jung, S., et al. (2014) · Science · doi:10.1126/science.1256271 · Cited by 776

Histone Methylation by PRC2 Is Inhibited by Active Chromatin Marks

Schmitges, F. W., Prusty, A. B., Faty, M., Stützer, A., Lingaraju, G. M., Aiwazian, J., Sack, R., Heß, D., Li, L., Zhou, S., et al. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.03.025 · Cited by 772

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiationPreprint

Dinger, M. E., Amaral, P., Mercer, T. R., Pang, K. C., Bruce, S. J., Gardiner, B., Askarian-Amiri, M., Ru, K., Soldà, G., Simons, C., et al. (2008) · Genome Research · doi:10.1101/gr.078378.108 · Cited by 753

Dedifferentiation, transdifferentiation and reprogramming: three routes to regeneration

Jopling, C., Boué, S., & Belmonte, J. C. I. (2011) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3043 · Cited by 750

Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos

Liu, X., Wang, C., Liu, W., Li, J., Li, C., Kou, X., Chen, J., Zhao, Y., Gao, H., Wang, H., et al. (2016) · Nature · doi:10.1038/nature19362 · Cited by 746

A long noncoding RNA protects the heart from pathological hypertrophy

Han, P., Li, W., Lin, C.-H., Yang, J., Shang, C., Nürnberg, S., Jin, K. K., Xu, W., Lin, C., Lin, C., et al. (2014) · Nature · doi:10.1038/nature13596 · Cited by 743

Intragenic DNA methylation prevents spurious transcription initiation

Neri, F., Rapelli, S., Krepelova, A., Incarnato, D., Parlato, C., Basile, G., Maldotti, M., Anselmi, F., & Oliviero, S. (2017) · Nature · doi:10.1038/nature21373 · Cited by 739

Chromatin structure analyses identify miRNA promotersPreprint

Ozsolak, F., Poling, L. L., Wang, Z., Liu, H., Liu, X., Roeder, R. G., Zhang, X., Song, J. S., & Fisher, D. E. (2008) · Genes & Development · doi:10.1101/gad.1706508 · Cited by 736

An integrated software system for analyzing ChIP-chip and ChIP-seq data

Ji, H., Jiang, H., Ma, W., Johnson, D. S., Myers, R., & Wong, W. H. (2008) · Nature Biotechnology · doi:10.1038/nbt.1505 · Cited by 722

Global Transcription in Pluripotent Embryonic Stem Cells

Efroni, S., Duttagupta, R., Cheng, J., Dehghani, H., Hoeppner, D. J., Dash, C., Bazett‐Jones, D. P., Grice, S. F. J. L., McKay, R. D. G., Buetow, K. H., et al. (2008) · Cell stem cell · doi:10.1016/j.stem.2008.03.021 · Cited by 719

Whole-Genome Analysis of Histone H3 Lysine 4 and Lysine 27 Methylation in Human Embryonic Stem Cells

Pan, G., Tian, S., Nie, J., Yang, C., Ruotti, V., Wei, H., Jonsdottir, G. A., Stewart, R., & Thomson, J. A. (2007) · Cell Stem Cell · doi:10.1016/j.stem.2007.08.003 · Cited by 711

Embryonic stem cell–specific microRNAs promote induced pluripotency

Judson, R. L., Babiarz, J., Venere, M., & Blelloch, R. H. (2009) · Nature Biotechnology · doi:10.1038/nbt.1535 · Cited by 702

Polycomb Group Proteins: Multi-Faceted Regulators of Somatic Stem Cells and Cancer

Sauvageau, M., & Sauvageau, G. (2010) · Cell Stem Cell · doi:10.1016/j.stem.2010.08.002 · Cited by 586

The role of mutations in epigenetic regulators in myeloid malignancies

Shih, A. H., Abdel-Wahab, O. I., Patel, J. P., & Levine, R. L. (2012) · Nature reviews. Cancer · doi:10.1038/nrc3343 · Cited by 696

Differential chromatin marking of introns and expressed exons by H3K36me3

Kolasinska-Zwierz, P., Down, T. A., Latorre, I. J., Liu, T., Liu, X. S., & Ahringer, J. (2009) · Nature Genetics · doi:10.1038/ng.322 · Cited by 699

Germline Competent Embryonic Stem Cells Derived from Rat Blastocysts

Li, P., Tong, C., Mehrian‐Shai, R., Li, J., Wu, N. L., Yan, Y., Maxson, R. E., Schulze, E. N., Song, H., Hsieh, C., et al. (2008) · Cell · doi:10.1016/j.cell.2008.12.006 · Cited by 686

Facultative Heterochromatin: Is There a Distinctive Molecular Signature?

Trojer, P., & Reinberg, D. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.09.011 · Cited by 686

Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa

Brykczynska, U., Hisano, M., Erkek, S., Ramos, L., Oakeley, E. J., Roloff, T. C., Beisel, C., Schübeler, D., Stadler, M. B., & Peters, A. H. F. M. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1821 · Cited by 680

Induced Pluripotent Stem Cell Generation Using a Single Lentiviral Stem Cell Cassette

Sommer, C. A., Stadtfeld, M., Murphy, G. J., Hochedlinger, K., Kotton, D. N., & Mostoslavsky, G. (2009) · Stem Cells · doi:10.1634/stemcells.2008-1075 · Cited by 676

Machine learning for integrating data in biology and medicine: principles, practice, and opportunities

Zitnik, M., Nguyen, F., Wang, B., Leskovec, J., Goldenberg, A., & Hoffman, M. M. (2019) · Information Fusion · doi:10.1016/j.inffus.2018.09.012 · Cited by 675

MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspecklesPreprint

Sunwoo, H., Dinger, M. E., Wilusz, J. E., Amaral, P., Mattick, J. S., & Spector, D. L. (2008) · Genome Research · doi:10.1101/gr.087775.108 · Cited by 672

Child Health, Developmental Plasticity, and Epigenetic Programming

Hochberg, Z., Feil, R., Constância, M., Fraga, M. F., Junien, C., Carel, J., Boileau, P., Bouc, Y. L., Deal, C., Lillycrop, K. A., et al. (2010) · Endocrine Reviews · doi:10.1210/er.2009-0039 · Cited by 657

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

Down, T. A., Rakyan, V. K., Turner, D., Flicek, P., Li, H., Kulesha, E., Gräf, S., Johnson, N., Herrero, J., Tomazou, E. M., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1414 · Cited by 650

Chromatin-modifying enzymes as modulators of reprogramming

Önder, T. T., Kara, N., Cherry, A. B. C., Sinha, A. U., Zhu, N., Bernt, K. M., Cahan, P., Mancarci, B. O., Unternaehrer, J., Gupta, P. B., et al. (2012) · Nature · doi:10.1038/nature10953 · Cited by 650

Transcription factors as readers and effectors of DNA methylation

Zhu, H., Wang, G., & Qian, J. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.83 · Cited by 649

Genome-wide Regulation of 5hmC, 5mC, and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells

Xu, Y., Wu, F., Tan, L., Kong, L., Xiong, L., Deng, J., Barbera, A. J., Zheng, L., Zhang, H., Huang, S., et al. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.04.005 · Cited by 647

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells

Wu, H., D’Alessio, A. C., Ito, S., Xia, K., Wang, Z., Cui, K., Zhao, K., Eve Sun, Y., & Zhang, Y. (2011) · Nature · doi:10.1038/nature09934 · Cited by 646

Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation

Cui, K., Zang, C., Roh, T., Schones, D. E., Childs, R. W., Peng, W., & Zhao, K. (2009) · Cell stem cell · doi:10.1016/j.stem.2008.11.011 · Cited by 646

CTCF-mediated functional chromatin interactome in pluripotent cells

Handoko, L., Han, X., Li, G., Ngan, C. Y., Chew, E. G. Y., Schnapp, M., Lee, C. W. H., Ye, C., Ping, J. L. H., Mulawadi, F. H., et al. (2011) · Nature Genetics · doi:10.1038/ng.857 · Cited by 646

Mechanisms of Stem Cell Self-Renewal

He, S., Nakada, D., & Morrison, S. J. (2009) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev.cellbio.042308.113248 · Cited by 644

Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs

Moran, V. A., Perera, R. J., & Khalil, A. M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks296 · Cited by 642

Chromatin organization marks exon-intron structure

Schwartz, S., Meshorer, E., & Ast, G. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1659 · Cited by 638

PRC2 is recurrently inactivated through EED or SUZ12 loss in malignant peripheral nerve sheath tumors

Lee, W., Teckie, S., Wiesner, T., Ran, L., Granada, C. N. P., Lin, M., Zhu, S., Cao, Z., Liang, Y., Sboner, A., et al. (2014) · Nature Genetics · doi:10.1038/ng.3095 · Cited by 637

Chromatin modifiers and remodellers: regulators of cellular differentiation

Chen, T., & Dent, S. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3607 · Cited by 636

ASXL1 Mutations Promote Myeloid Transformation through Loss of PRC2-Mediated Gene Repression

Abdel-Wahab, O. I., Adli, M., LaFave, L. M., Gao, J., Hricik, T., Shih, A. H., Pandey, S., Patel, J. P., Chung, Y. R., Koche, R. P., et al. (2012) · Cancer Cell · doi:10.1016/j.ccr.2012.06.032 · Cited by 636

Somatic mutations at EZH2 Y641 act dominantly through a mechanism of selectively altered PRC2 catalytic activity, to increase H3K27 trimethylation

Yap, D., Chu, J., Berg, T., Schapira, M., Cheng, S., Moradian, A., Morin, R. D., Mungall, A. J. J., Meissner, B., Boyle, M., et al. (2010) · Blood · doi:10.1182/blood-2010-11-321208 · Cited by 633

Posttranscriptional Gene Regulation by Long Noncoding RNA

Yoon, J., Abdelmohsen, K., & Gorospe, M. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2012.11.024 · Cited by 632

Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana

Zhang, X., Bernatavichute, Y. V., Cokus, S. J., Pellegrini, M. A., & Jacobsen, S. E. (2009) · Genome biology · doi:10.1186/gb-2009-10-6-r62 · Cited by 632

Whole-Genome Mapping of Histone H3 Lys4 and 27 Trimethylations Reveals Distinct Genomic Compartments in Human Embryonic Stem Cells

Zhao, X. D., Han, X., Chew, J. L., Liu, J., Chiu, K. P., Choo, A. B. H., Orlov, Y. L., Sung, W.-K. K., Shahab, A., Kuznetsov, V. A., et al. (2007) · Cell stem cell · doi:10.1016/j.stem.2007.08.004 · Cited by 626

CpG islands influence chromatin structure via the CpG-binding protein Cfp1

Thomson, J. P., Skene, P. J., Selfridge, J., Clouaire, T., Guy, J., Webb, S., Kerr, A. R. W., Deaton, A., Andrews, R., James, K. D., et al. (2010) · Nature · doi:10.1038/nature08924 · Cited by 625

Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

Wamstad, J. A., Alexander, J. M., Truty, R., Shrikumar, A., Li, F., Eilertson, K. E., Ding, H., Wylie, J. N., Pico, A. R., Capra, J. A., et al. (2012) · Cell · doi:10.1016/j.cell.2012.07.035 · Cited by 624

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

Schmidt, D., Schwalie, P. C., Wilson, M. D., Ballester, B., Gonçalves, Â., Kutter, C., Brown, G. D., Marshall, A., Flicek, P., & Odom, D. T. (2012) · Cell · doi:10.1016/j.cell.2011.11.058 · Cited by 620

Meiotic recombination in mammals: localization and regulation

Baudat, F., Imai, Y., & de Massy, B. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3573 · Cited by 616

Epigenetic Silencing of MicroRNA-34b/c and B-Cell Translocation Gene 4 Is Associated with CpG Island Methylation in Colorectal Cancer

Toyota, M., Suzuki, H., Sasaki, Y., Maruyama, R., Imai, K., Shinomura, Y., & Tokino, T. (2008) · Cancer Research · doi:10.1158/0008-5472.can-08-0325 · Cited by 615

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

Yaffe, E., & Tanay, A. (2011) · Nature Genetics · doi:10.1038/ng.947 · Cited by 614

Genomic views of distant-acting enhancers

Visel, A., Rubin, E. M., & Pennacchio, L. A. (2009) · Nature · doi:10.1038/nature08451 · Cited by 610

Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host

Timp, W., & Feinberg, A. P. (2013) · Nature reviews. Cancer · doi:10.1038/nrc3486 · Cited by 611

Next-generation genomics: an integrative approach

Hawkins, R. D., Hon, G. C., & Ren, B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2795 · Cited by 608

BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals

Poser, I., Sarov, M., Hutchins, J. R. A., Hèriché, J.-K., Toyoda, Y., Pozniakovsky, A., Weigl, D., Nitzsche, A., Hegemann, B., Bird, A. W., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1199 · Cited by 605

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cellsPreprint

Wu, H., D’Alessio, A. C., Ito, S., Wang, Z., 崔凯荣, Zhao, K., Sun, Y. E., & Zhang, Y. (2011) · Genes & Development · doi:10.1101/gad.2036011 · Cited by 603

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression

Engreitz, J., Ollikainen, N., & Guttman, M. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.126 · Cited by 595

JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells

Pasini, D., Cloos, P. A., Walfridsson, J., Olsson, L., Bukowski, J., Johansen, J. V., Bak, M., Tommerup, N., Rappsilber, J., & Helin, K. (2010) · Nature · doi:10.1038/nature08788 · Cited by 584

RYBP-PRC1 Complexes Mediate H2A Ubiquitylation at Polycomb Target Sites Independently of PRC2 and H3K27me3

Tavares, L., Dimitrova, E., Oxley, D., Webster, J. A., Poot, R. A., Demmers, J., Bezstarosti, K., Taylor, S., Ura, H., Koide, H., et al. (2012) · Cell · doi:10.1016/j.cell.2011.12.029 · Cited by 583

Understanding the relationship between DNA methylation and histone lysine methylation

Rose, N. R., & Klose, R. J. (2014) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2014.02.007 · Cited by 576

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

Hiratani, I., Ryba, T., Itoh, M., Yokochi, T., Schwaiger, M., Chang, C., Lyou, Y., Townes, T. M., Schübeler, D., & Gilbert, D. M. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060245 · Cited by 576

Coordinating cell proliferation and differentiation: Antagonism between cell cycle regulators and cell type-specific gene expression

Ruijtenberg, S., & van den Heuvel, S. (2016) · Cell Cycle · doi:10.1080/15384101.2015.1120925 · Cited by 577

Regulation and function of DNA methylation in plants and animals

He, X., Chen, T., & Zhu, J. (2011) · Cell Research · doi:10.1038/cr.2011.23 · Cited by 574

Ring1B Compacts Chromatin Structure and Represses Gene Expression Independent of Histone Ubiquitination

Eskeland, R., Leeb, M., Grimes, G. R., Kress, C., Boyle, S., Sproul, D., Gilbert, N., Fan, Y., Skoultchi, A. I., Wutz, A., et al. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.02.032 · Cited by 571

Computation for ChIP-seq and RNA-seq studies

Pepke, S., Wold, B. J., & Mortazavi, A. (2009) · Nature Methods · doi:10.1038/nmeth.1371 · Cited by 568

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

He, G., Zhu, X., Elling, A. A., Chen, L., Wang, X., Guo, L. P., Liang, M., He, H., Zhang, H., Chen, F., et al. (2010) · The Plant Cell · doi:10.1105/tpc.109.072041 · Cited by 568

Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers

Thomson, M. W., Liu, S. J., Zou, L.-N., Smith, Z., Meissner, A., & Ramanathan, S. (2011) · Cell · doi:10.1016/j.cell.2011.05.017 · Cited by 566

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

Zentner, G. E., Tesar, P. J., & Scacheri, P. C. (2011) · Genome Research · doi:10.1101/gr.122382.111 · Cited by 564

Mechanisms regulating zygotic genome activation

Schulz, K. N., & Harrison, M. M. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0087-x · Cited by 564

Wdr5 Mediates Self-Renewal and Reprogramming via the Embryonic Stem Cell Core Transcriptional Network

Ang, Y.-S., Tsai, S., Lee, D., Monk, J. M., Su, J., Ratnakumar, K., Ding, J., Ge, Y., Darr, H., Chang, B., et al. (2011) · Cell · doi:10.1016/j.cell.2011.03.003 · Cited by 559

Roles and regulation of histone methylation in animal development

Jambhekar, A., Dhall, A., & Shi, Y. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0151-1 · Cited by 556

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

Illingworth, R. S., Gruenewald-Schneider, U., Webb, S., Kerr, A. R. W., James, K. D., Turner, D. J., Smith, C., Harrison, D. J., Andrews, R., & Bird, A. P. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001134 · Cited by 550

Mapping Human Epigenomes

Rivera, C. M., & Ren, B. (2013) · Cell · doi:10.1016/j.cell.2013.09.011 · Cited by 550

Jarid2/Jumonji Coordinates Control of PRC2 Enzymatic Activity and Target Gene Occupancy in Pluripotent Cells

Peng, J. C., Valouev, A., Swigut, T., Zhang, J., Zhao, Y., Sidow, A., & Wysocka, J. (2009) · Cell · doi:10.1016/j.cell.2009.12.002 · Cited by 548

Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation

Edmunds, J. W., Mahadevan, L. C., & Clayton, A. L. (2008) · The EMBO Journal · doi:10.1038/sj.emboj.7601967 · Cited by 547

Chromatin modifications as determinants of muscle stem cell quiescence and chronological aging

Liu, L., Cheung, T. H., Charville, G. W., Hurgo, B. M. C., Leavitt, T., Shih, J., Brunet, A., & Rando, T. A. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.05.043 · Cited by 544

From neural development to cognition: unexpected roles for chromatin

Ronan, J. L., Wu, W., & Crabtree, G. R. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3413 · Cited by 544

H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells

Karmodiya, K., Krebs, A. R., Oulad‐Abdelghani, M., Kimura, H., & Tora, L. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-424 · Cited by 544

Polycomb-Dependent H3K27me1 and H3K27me2 Regulate Active Transcription and Enhancer Fidelity

Ferrari, K. J., Scelfo, A., Jammula, S., Cuomo, A., Barozzi, I., Stützer, A., Fischle, W., Bonaldi, T., & Pasini, D. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.10.030 · Cited by 540

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

Jothi, R., Cuddapah, S., Barski, A., Cui, K., & Zhao, K. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn488 · Cited by 539

TET2 promotes histone O-GlcNAcylation during gene transcription

Chen, Q., Chen, Y., Bian, C., Fujiki, R., & Yu, X. (2012) · Nature · doi:10.1038/nature11742 · Cited by 537

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

Mikkelsen, T. S., Zhao, X. D., Zhang, X., Wang, L., Gimble, J. M., Lander, E. S., & Rosen, E. D. (2010) · Cell · doi:10.1016/j.cell.2010.09.006 · Cited by 538

DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs

Karimi, M. M., Goyal, P., Maksakova, I. A., Bilenky, M., Leung, D., Tang, J. X., Shinkai, Y., Mager, D. L., Jones, S., Hirst, M., et al. (2011) · Cell Stem Cell · doi:10.1016/j.stem.2011.04.004 · Cited by 535

Deconstructing repression: evolving models of co-repressor action

Perissi, V., Jepsen, K., Glass, C. K., & Rosenfeld, M. G. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2736 · Cited by 532

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

Kelley, D., & Rinn, J. (2012) · Genome Biology · doi:10.1186/gb-2012-13-11-r107 · Cited by 531

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

Schmidt, D., Wilson, M. D., Spyrou, C., Brown, G. D., Hadfield, J., & Odom, D. T. (2009) · Methods · doi:10.1016/j.ymeth.2009.03.001 · Cited by 530

Epigenetic balance of gene expression by Polycomb and COMPASS families

Piunti, A., & Shilatifard, A. (2016) · Science · doi:10.1126/science.aad9780 · Cited by 524

Deterministic direct reprogramming of somatic cells to pluripotency

Rais, Y., Zviran, A., Geula, S., Gafni, O., Chomsky, E., Viukov, S., Mansour, A. A., Caspi, I., Krupalnik, V., Zerbib, M., et al. (2013) · Nature · doi:10.1038/nature12587 · Cited by 522

Overview of Histone Modification

Zhang, Y., Sun, Z., Jia, J., Du, T., Zhang, N., Tang, Y., Fang, Y., & Fang, D. (2020) · Advances in experimental medicine and biology · doi:10.1007/978-981-15-8104-5_1 · Cited by 530

Jarid2 and PRC2, partners in regulating gene expressionPreprint

Li, G., Margueron, R., Ku, M., Chambon, P., Bernstein, B., & Reinberg, D. (2010) · Genes & Development · doi:10.1101/gad.1886410 · Cited by 521

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

Guo, H., Zhu, P., Wu, X., Li, X., Wen, L., & Tang, F. (2013) · Genome Research · doi:10.1101/gr.161679.113 · Cited by 518

High-resolution mapping of copy-number alterations with massively parallel sequencing

Chiang, D. Y., Getz, G. A., Jaffe, D. B., O'Kelly, M., Zhao, X., Carter, S. L., Russ, C., Nusbaum, C., Meyerson, M. M., & Lander, E. S. (2008) · Nature Methods · doi:10.1038/nmeth.1276 · Cited by 516

DOT1L/KMT4 Recruitment and H3K79 Methylation Are Ubiquitously Coupled with Gene Transcription in Mammalian Cells

Steger, D. J., Lefterova, M. I., Ying, L., Stonestrom, A. J., Schupp, M., Zhuo, D. X., Vakoc, A. L., Kim, J., Chen, J., Lazar, M. A., et al. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.02076-07 · Cited by 515

DNA methylation and methyl-CpG binding proteins: developmental requirements and function

Bogdanović, O., & Veenstra, G. J. C. (2009) · Chromosoma · doi:10.1007/s00412-009-0221-9 · Cited by 503

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

Bonn, S., Zinzen, R. P., Girardot, C., Gustafson, E. H., Perez-Gonzalez, A., Delhomme, N., Ghavi-Helm, Y., Wilczyński, B., Riddell, A., & Furlong, E. E. M. (2012) · Nature Genetics · doi:10.1038/ng.1064 · Cited by 502

KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands

Farcas, A. M., Blackledge, N. P., Sudbery, I. M., Long, H. K., McGouran, J. F., Rose, N. R., Lee, S., Sims, D., Cerase, A., Sheahan, T. W., et al. (2012) · eLife · doi:10.7554/elife.00205 · Cited by 502

The molecular principles of gene regulation by Polycomb repressive complexes

Blackledge, N. P., & Klose, R. J. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00398-y · Cited by 500

Genome-wide Analysis Reveals TET- and TDG-Dependent 5-Methylcytosine Oxidation Dynamics

Shen, L., Wu, H., Diep, D., Yamaguchi, S., D’Alessio, A. C., Fung, H.-L., Zhang, K., & Zhang, Y. (2013) · Cell · doi:10.1016/j.cell.2013.04.002 · Cited by 497

The epigenomic era opens

Baylin, S. B., & Schuebel, K. E. (2007) · Nature · doi:10.1038/448548a · Cited by 47

Discovering and mapping chromatin states using a tree hidden Markov model

Biesinger, J., Wang, Y., & Xie, X. S. (2013) · F1000Research · doi:10.7490/f1000research.1093084.1

Genome-wide mapping of chromatin state of mouse forelimbs

Kioussi, C., Gross, M., Eng, D. G., Vogel, W., & Flann, N. S. (2014) · Open Access Bioinformatics · doi:10.2147/oab.s59043 · Cited by 4

Profiling chromatin states using single-cell itChIP-seq

Ai, S., Xiong, H., Li, C. C., Luo, Y., Shi, Q., Liu, Y., Yu, X., Li, C., & He, A. (2019) · Nature Cell Biology · doi:10.1038/s41556-019-0383-5 · Cited by 140

Chromatin state maps: new technologies, new insights

Mendenhall, E. M., & Bernstein, B. (2008) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2008.01.010 · Cited by 89