The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.
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.
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
“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]
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]
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]
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
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
Cited by
Sorted by citations
Items 601–700 of 1,026
Han, H., Cortez, C. C., Yang, X., Nichols, P. W., Jones, P. A., & Liang, G. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr356 · Cited by 195
Tissue-specific disallowance of housekeeping genes: The other face of cell differentiationPreprint
Thorrez, L., Laudadio, I., Deun, K. V., Quintens, R., Hendrickx, N., Granvik, M., Lemaire, K., Schraenen, A., Lommel, L. V., Lehnert, S., et al. (2010) · Genome Research · doi:10.1101/gr.109173.110 · Cited by 193
Isolation of neuronal chromatin from brain tissue
Jiang, Y., Matevossian, A., Huang, H.-S., Straubhaar, J., & Akbarian, S. (2008) · BMC Neuroscience · doi:10.1186/1471-2202-9-42 · Cited by 193
A Histone Methylation Network Regulates Transgenerational Epigenetic Memory in C. elegans
Greer, E. L., Beese‐Sims, S. E., Brookes, E., Spadafora, R., Zhu, Y., Rothbart, S. B., Aristizábal-Corrales, D., Chen, S., Badeaux, A. I., Jin, Q., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.02.044 · Cited by 192
Vieira, M. S., Santos, A. K., Vasconcellos, R., Goulart, V. A. M., Parreira, R. C., Kihara, A. H., Ulrich, H., & Resende, R. R. (2018) · Biotechnology Advances · doi:10.1016/j.biotechadv.2018.08.002 · Cited by 192
The nucleosome remodeling and deacetylase complex in development and disease
Basta, J., & Rauchman, M. (2015) · Translational Research · doi:10.1016/j.trsl.2014.05.003 · Cited by 191
Transposable elements in the mammalian germline: a comfortable niche or a deadly trap?
Zamudio, N., & Bourc’his, D. (2010) · Heredity · doi:10.1038/hdy.2010.53 · Cited by 191
Moving AHEAD with an international human epigenome project
Jones, P. A., Archer, T., Baylin, S. B., Beck, S., Berger, S. L., Bernstein, B., Carpten, J. D., Clark, S. J., Costello, J., Doerge, R. W., et al. (2008) · Nature · doi:10.1038/454711a · Cited by 191
Self-citationLo, P., & Sukumar, S. V. (2008) · Pharmacogenomics · doi:10.2217/14622416.9.12.1879 · Cited by 191
Pol II and its associated epigenetic marks are present at Pol III–transcribed noncoding RNA genes
Barski, A., Chepelev, I., Liko, D., Cuddapah, S., Fleming, A. B., Birch, J. L., Cui, K., White, R. J., & Zhao, K. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1806 · Cited by 191
Rowe, H. M., Kapopoulou, A., Corsinotti, A., Fasching, L., Macfarlan, T. S., Tarabay, Y., Viville, S., Jakobsson, J., Pfaff, S. L., & Trono, D. (2012) · Genome Research · doi:10.1101/gr.147678.112 · Cited by 190
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
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
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
Bivalent Chromatin Marks Developmental Regulatory Genes in the Mouse Embryonic Germline In Vivo
Sachs, M. M., Onodera, C. S., Blaschke, K., Ebata, K. T., Song, J. S., & Ramalho‐Santos, M. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.04.032 · Cited by 187
Lin, C., Garrett, A. S., Kumar, B. D., Smith, E. R., Gogol, M., Seidel, C. W., Krumlauf, R. K., & Shilatifard, A. (2011) · Genes & Development · doi:10.1101/gad.2059211 · Cited by 187
DNA methylation and gene expression
Siegfried, Z., & Simon, I. (2009) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.64 · Cited by 186
Histone demethylase KDM5A is an integral part of the core Notch–RBP-J repressor complexPreprint
Liefke, R., Oswald, F., Alvarado, C., Ferrés-Marcó, D., Mittler, G., Rodriguez, P., Domínguez, M., & Borggrefe, T. (2010) · Genes & Development · doi:10.1101/gad.563210 · Cited by 187
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
Visualizing biologically active small molecules in cells using click chemistry
Cañeque, T., Müller, S., & Rodriguez, R. (2018) · Nature Reviews Chemistry · doi:10.1038/s41570-018-0030-x · Cited by 185
Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview
Geis, F. K., & Goff, S. P. (2020) · Viruses · doi:10.3390/v12080884 · Cited by 188
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
Intronic RNAs mediate EZH2 regulation of epigenetic targets
Guil, S., Soler, M., Portela, A., Carrere-Molina, J., Fonalleras, E., Gómez, A., Villanueva, A., & Esteller, M. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2315 · Cited by 183
Transcriptional Regulatory Circuits: Predicting Numbers from Alphabets
Kim, H. D., Shay, T., O’Shea, E. K., & Regev, A. (2009) · Science · doi:10.1126/science.1171347 · Cited by 182
Epigenetic Control of Stem Cell Potential during Homeostasis, Aging, and Disease
Beerman, I., & Rossi, D. J. (2015) · Cell stem cell · doi:10.1016/j.stem.2015.05.009 · Cited by 182
Yaffe, E., Farkash-Amar, S., Polten, A., Yakhini, Z., Tanay, A., & Simon, I. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001011 · Cited by 182
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
Histone H3K9 methyltransferase G9a represses PPARγ expression and adipogenesis
Wang, L., Xu, S., Lee, J., Baldridge, A., Grullon, S., Peng, W., & Ge, K. (2012) · The EMBO Journal · doi:10.1038/emboj.2012.306 · Cited by 182
Mundade, R., Özer, H. G., Han, W., Prabhu, L., & Lu, T. (2014) · Cell Cycle · doi:10.4161/15384101.2014.949201 · Cited by 181
Tahira, A. C., Kubrusly, M. S., Faria, M. F., Dazzani, B., Fonseca, R. S., Maracaja‐Coutinho, V., Verjovski‐Almeida, S., Machado, M. C. C., & Reis, E. M. R. (2011) · Molecular Cancer · doi:10.1186/1476-4598-10-141 · Cited by 182
Discovery and Annotation of Functional Chromatin Signatures in the Human Genome
Hon, G. C., Wang, W., & Ren, B. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000566 · Cited by 181
KDM5B regulates embryonic stem cell self‐renewal and represses cryptic intragenic transcription
Xie, L., Pelz, C., Wang, W., Bashar, A., Varlamova, O., Shadle, S. C., & Impey, S. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.91 · Cited by 180
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
Minireview: PPARγ as the target of obesogens
Janesick, A., & Blumberg, B. (2011) · The Journal of Steroid Biochemistry and Molecular Biology · doi:10.1016/j.jsbmb.2011.01.005 · Cited by 179
Bredfeldt, T., Greathouse, K. L., Safe, S. H., Hung, M., Bedford, M. T., & Walker, C. L. (2010) · Molecular Endocrinology · doi:10.1210/me.2009-0438 · Cited by 179
Aberrant DNA methylation patterns of spermatozoa in men with unexplained infertility
Urdinguio, R. G., Bayón, G. F., Dmitrijeva, M., Toraño, E. G., Bravo, C., Fraga, M. F., Bassas, L., Larriba, S., & Fernández, A. F. (2015) · Human Reproduction · doi:10.1093/humrep/dev053 · Cited by 180
Bioinformatics analysis of mass spectrometry‐based proteomics data sets
Kumar, C., & Mann, M. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.03.035 · Cited by 178
Loss of Asxl1 leads to myelodysplastic syndrome–like disease in mice
Wang, J., Li, Z., He, Y., Pan, F., Shi, C., Rhodes, S. D., Nguyen, L., Yuan, J., Jiang, L., Yang, X., et al. (2013) · Blood · doi:10.1182/blood-2013-05-500272 · Cited by 178
Hunter, R. G., Murakami, G., Dewell, S. B., Seligsohn, M., Baker, M. E. R., Datson, N. A., McEwen, B. S., & Pfaff, D. W. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1215810109 · Cited by 178
Marques, A. C., Hughes, J. R., Graham, B., Kowalczyk, M. S., Higgs, D. R., & Ponting, C. P. (2013) · Genome biology · doi:10.1186/gb-2013-14-11-r131 · Cited by 178
Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism
Nitsch, S., Shahidian, L. Z., & Schneider, R. (2021) · EMBO Reports · doi:10.15252/embr.202152774 · Cited by 180
Maksakova, I. A., Mager, D. L., & Reiss, D. (2008) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-008-8494-3 · Cited by 177
Bell, O., Wirbelauer, C., Hild, M., Scharf, A. N. D., Schwaiger, M., MacAlpine, D. M., Zilbermann, F., van Leeuwen, F., Bell, S. P., Imhof, A., et al. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601926 · Cited by 177
Transcriptional regulation of mammalian miRNA genes
Schanen, B. C., & Li, X. (2010) · Genomics · doi:10.1016/j.ygeno.2010.10.005 · Cited by 176
Memories from the Polycomb Group Proteins
Lanzuolo, C., & Orlando, V. (2012) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155603 · Cited by 176
MLL2 conveys transcription-independent H3K4 trimethylation in oocytes
Hanna, C. W., Taudt, A., Huang, J., Gahurová, L., Kranz, A., Andrews, S., Dean, W., Stewart, A. F., Colomé‐Tatché, M., & Kelsey, G. (2017) · Nature Structural & Molecular Biology · doi:10.1038/s41594-017-0013-5 · Cited by 176
A glimpse into past, present, and future DNA sequencing
Morey, M., Marmiesse, A. F., Castiñeiras, D. E., Fraga, J. M., Couce, M. L., & Cocho, J. A. (2013) · Molecular Genetics and Metabolism · doi:10.1016/j.ymgme.2013.04.024 · Cited by 177
Harmston, N., Ing‐Simmons, E., Tan, G., Perry, M., Merkenschlager, M., & Lenhard, B. (2017) · Nature Communications · doi:10.1038/s41467-017-00524-5 · Cited by 175
Atrx promotes heterochromatin formation at retrotransposons
Sadic, D., Schmidt, K. M., Groh, S., Kondofersky, I., Ellwart, J. W., Fuchs, C., Theis, F. J., & Schotta, G. (2015) · EMBO Reports · doi:10.15252/embr.201439937 · Cited by 174
Epigenetics of breast cancer: Biology and clinical implication in the era of precision medicine
Pasculli, B., Barbano, R., & Parrella, P. (2018) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2018.01.007 · Cited by 174
Using ChIP-Seq Technology to Generate High-Resolution Profiles of Histone Modifications
O’Geen, H., Echipare, L., & Farnham, P. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-316-5_20 · Cited by 174
Epigenetic alterations in autoimmune rheumatic diseases
Ballestar, E. (2011) · Nature Reviews Rheumatology · doi:10.1038/nrrheum.2011.16 · Cited by 173
High-Resolution Enzymatic Mapping of Genomic 5-Hydroxymethylcytosine in Mouse Embryonic Stem Cells
Sun, Z., Terragni, J., Borgaro, J. G., Liu, Y., Yu, L., Guan, S., Wang, H., Sun, D., Cheng, X., Zhu, Z., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.01.001 · Cited by 173
Human IL-31 is induced by IL-4 and promotes TH2-driven inflammation
Stott, B., Lavender, P., Lehmann, S., Pennino, D., Durham, S., & Schmidt‐Weber, C. B. (2013) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2013.03.050 · Cited by 173
Differential roles of Sall4 isoforms in embryonic stem cell pluripotency
Rao, S., Zhen, S., Roumiantsev, S., McDonald, L. T., Yuan, G.-C., & Orkin, S. H. (2010) · Molecular and Cellular Biology · doi:10.1128/mcb.00419-10 · Cited by 173
Epigenetic Regulation by Lysine Demethylase 5 (KDM5) Enzymes in Cancer
Blair, L. P., Cao, J. P., Zou, M. R., Sayegh, J., & Yan, Q. (2011) · Cancers · doi:10.3390/cancers3011383 · Cited by 172
Delacroix, L., Moutier, E., Altobelli, G., Gras, S. L., Poch, O., Choukrallah, M.-A., Bertin, I., Jost, B., & Davidson, I. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.00756-09 · Cited by 172
Shaw, T., & Martin, P. (2009) · The EMBO Reports · doi:10.1038/embor.2009.102 · Cited by 171
GlcNAcylation of a histone methyltransferase in retinoic-acid-induced granulopoiesis
Fujiki, R., Chikanishi, T., Hashiba, W., Ito, H., Takada, I., Roeder, R. G., Kitagawa, H., & Kato, S. (2009) · Nature · doi:10.1038/nature07954 · Cited by 171
RetractedUnraveling Epigenetic Regulation in Embryonic Stem Cells
Bibikova, M. V., Laurent, L. C., Ren, B., Loring, J. F., & Fan, J. (2008) · Cell stem cell · doi:10.1016/j.stem.2008.01.005 · Cited by 171
Genic and Global Functions for Paf1C in Chromatin Modification and Gene Expression in Arabidopsis
Oh, S., Park, S., & van Nocker, S. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000077 · Cited by 170
Acetylation of histone H3 at lysine 64 regulates nucleosome dynamics and facilitates transcription
Cerbo, V. D., Mohn, F., Ryan, D., Montellier, E., Kacem, S., Tropberger, P., Kallis, E., Holzner, M., Hoerner, L., Feldmann, A., et al. (2014) · eLife · doi:10.7554/elife.01632 · Cited by 171
Systematic evaluation of factors influencing ChIP-seq fidelity
Chen, Y., Nègre, N., Li, Q., Mieczkowska, J. O., Slattery, M. G., Liu, T., Zhang, Y., Kim, T.-K., He, H. H., Zieba, J. T., et al. (2012) · Nature Methods · doi:10.1038/nmeth.1985 · Cited by 170
Self-citationTransposable elements in the mammalian embryo: pioneers surviving through stealth and service
Gerdes, P., Richardson, S. R., Mager, D. L., & Faulkner, G. J. (2016) · Genome Biology · doi:10.1186/s13059-016-0965-5 · Cited by 156
The control of gene expression and cell identity by H3K9 trimethylation
Ninova, M., Tóth, K. F., & Aravin, A. A. (2019) · Development · doi:10.1242/dev.181180 · Cited by 170
The Transcriptional and Epigenetic Landscape of Cancer Cell Lineage Plasticity
Davies, A., Zoubeidi, A., Beltran, H., & Selth, L. A. (2023) · Cancer Discovery · doi:10.1158/2159-8290.cd-23-0225 · Cited by 170
Pampari, A., Shcherbina, A., Kvon, E. Z., Kosicki, M., Nair, S., Kundu, S., Kathiria, A. S., Risca, V. I., Kuningas, K., Alasoo, K., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.25.630221 · Cited by 183
Genomic location analysis by ChIP‐Seq
Barski, A., & Zhao, K. (2009) · Journal of Cellular Biochemistry · doi:10.1002/jcb.22077 · Cited by 169
Ke, X., Qu, Y., Rostad, K., Li, W., Lin, B., HALVORSEN, O. J., Haukaas, S. A., Jonassen, I., Petersen, K., Goldfinger, N., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004687 · Cited by 169
Targeted silencing of the oncogenic transcription factor SOX2 in breast cancer
Stolzenburg, S., Rots, M. G., Beltrán, A. S., Rivenbark, A. G., Yuan, X., Qian, H., Strahl, B. D., & Blancafort, P. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks360 · Cited by 169
Krendl, C., Shaposhnikov, D., Rishko, V. M., Ori, C., Ziegenhain, C., Sass, S., Simon, L. M., Müller, N. S., Straub, T., Brooks, K. E., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1708341114 · Cited by 169
Wong, C., Wei, L., Law, C., Ho, D. W., Tsang, F. H., Au, S. L., Sze, K. M., Lee, J. M., Wong, C. C., & Ng, I. O. (2015) · Hepatology · doi:10.1002/hep.28304 · Cited by 168
Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stationsPreprint
Pinter, S. F., Sadreyev, R. I., Yildirim, E., Jeon, Y., Ohsumi, T. K., Borowsky, M. L., & Lee, J. T. (2012) · Genome Research · doi:10.1101/gr.133751.111 · Cited by 168
KAT5 tyrosine phosphorylation couples chromatin sensing to ATM signalling
Kaidi, A., & Jackson, S. P. (2013) · Nature · doi:10.1038/nature12201 · Cited by 167
RetractedWes, P. D., Holtman, I. R., Boddeke, E. W. G. M., Möller, T., & Eggen, B. J. L. (2016) · Glia · doi:10.1002/glia.22866 · Cited by 167
Control of embryonic stem cell lineage commitment by core promoter factor, TAF3
Liu, Z., Scannell, D. R., Eisen, M. B., & Tjian, R. (2011) · Cell · doi:10.1016/j.cell.2011.08.005 · Cited by 167
Sharov, A. A., Masui, S., Sharova, L. V., Piao, Y., Aiba, K., Matoba, R., Li, X., Niwa, H., & Ko, M. S. H. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-269 · Cited by 167
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
Genome-wide assessment of differential roles for p300 and CBP in transcription regulation
Ramos, Y. F., Hestand, M. S., Verlaan, M., Krabbendam, E., Ariyürek, Y., van Galen, M., van Dam, H., van Ommen, G. B., den Dunnen, J. T., ZANTEMA, A., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq184 · Cited by 166
Yang, X., Karuturi, R. K. M., Sun, F., Aau, M., Yu, K., Shao, R., Miller, L. D., Tan, P. B. O., & Yu, Q. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005011 · Cited by 166
Human tRNA genes function as chromatin insulators
Raab, J. R., Chiu, J., Zhu, J., Katzman, S. J., Kurukuti, S., Wade, P. A., Haussler, D. H., & Kamakaka, R. T. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.406 · Cited by 166
Tiwari, V. K., Burger, L., Nikoletopoulou, V., Deogracias, R., Thakurela, S., Wirbelauer, C., Kaut, J., Terranova, R., Hoerner, L., Mielke, C., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1119798109 · Cited by 166
Rapid and reversible epigenome editing by endogenous chromatin regulators
Braun, S. M. G., Kirkland, J. G., Chory, E. J., Husmann, D., Calarco, J. P., & Crabtree, G. R. (2017) · Nature Communications · doi:10.1038/s41467-017-00644-y · Cited by 166
Kong, X., Chen, J., Xie, W., Brown, S. M., Cai, Y., Wu, K., Fan, D., Nie, Y., Yegnasubramanian, S., Tiedemann, R. L., et al. (2019) · Cancer Cell · doi:10.1016/j.ccell.2019.03.003 · Cited by 166
Rivera‐Mulia, J. C., Buckley, Q., Sasaki, T., Zimmerman, J., Didier, R., Nazor, K. L., Loring, J. F., Lian, Z., Weissman, S. M., Robins, A. J., et al. (2015) · Genome Research · doi:10.1101/gr.187989.114 · Cited by 166
Tee, W.-W., Shen, S. S., Oksuz, O., Narendra, V., & Reinberg, D. (2014) · Cell · doi:10.1016/j.cell.2014.01.009 · Cited by 165
Grossman, S. R., Zhang, X., Wang, L., Engreitz, J., Melnikov, A., Rogov, P., Tewhey, R., Isakova, A., Deplancke, B., Bernstein, B. E., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1621150114 · Cited by 165
Self-citationGlobal Survey of Genomic Imprinting by Transcriptome Sequencing
Babak, T., DeVeale, B., Armour, C. D., Raymond, C. K., Cleary, M. A., van der Kooy, D., Johnson, J. M., & Lim, L. P. (2008) · Current Biology · doi:10.1016/j.cub.2008.09.044 · Cited by 165
Blackledge, N. P., & Klose, R. J. (2011) · Epigenetics · doi:10.4161/epi.6.2.13640 · Cited by 165
Retrotransposon-Induced Heterochromatin Spreading in the Mouse Revealed by Insertional Polymorphisms
Rebollo, R., Karimi, M. M., Bilenky, M., Gagnier, L., Miceli-Royer, K., Zhang, Y., Goyal, P., Keane, T., Jones, S. J. M., Hirst, M., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002301 · Cited by 165
Epigenome Mapping in Normal and Disease States
Maunakea, A. K., Chepelev, I., & Zhao, K. (2010) · Circulation Research · doi:10.1161/circresaha.110.222463 · Cited by 165
Histone methyltransferase SETD2 modulates alternative splicing to inhibit intestinal tumorigenesis
Yuan, H., Li, N., Fu, D., Ren, J., Hui, J., Peng, J., Liu, Y., Qiu, T., Jiang, M., Pan‐Hammarström, Q., et al. (2017) · Journal of Clinical Investigation · doi:10.1172/jci94292 · Cited by 165
Structural basis for histone H3 Lys 27 demethylation by UTX/KDM6APreprint
Sengoku, T., & Yokoyama, S. (2011) · Genes & Development · doi:10.1101/gad.172296.111 · Cited by 165
TGF‐β control of stem cell differentiation genes
Massagué, J., & Xi, Q. (2012) · FEBS Letters · doi:10.1016/j.febslet.2012.03.023 · Cited by 164
Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes
Escoubet‐Lozach, L., Benner, C. W., Kaikkonen, M. U., Lozach, J., Heinz, S., Spann, N. J., Crotti, A., Stender, J. D., Ghisletti, S., Reichart, D. R., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002401 · Cited by 165
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
Crosstalk of Oncogenic Signaling Pathways during Epithelial–Mesenchymal Transition
Lindsey, S. C., & Langhans, S. A. (2014) · Frontiers in Oncology · doi:10.3389/fonc.2014.00358 · Cited by 163
Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors
Adli, M., Zhu, J., & Bernstein, B. (2010) · Nature Methods · doi:10.1038/nmeth.1478 · Cited by 163
Self-citationZhu, C., Gao, Y., Guo, H., Xia, B., Song, J., Wu, X., Zeng, H., Kee, K., Tang, F., & Yi, C. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.02.013 · Cited by 164
Chen, H., Tian, Y., Shu, W., Bo, X., & Wang, S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0041374 · Cited by 161
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
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
