The DOI matches its Crossref record; 66 of the 67 references it cites were found in a registry or an index.
Mapping and analysis of chromatin state dynamics in nine human cell types
Open accessAbstract
Chromatin profiling has emerged as a powerful means of genome annotation and detection of regulatory activity. The approach is especially well suited to the characterization of non-coding portions of the genome, which critically contribute to cellular phenotypes yet remain largely uncharted. Here we map nine chromatin marks across nine cell types to systematically characterize regulatory elements, their cell-type specificities and their functional interactions. Focusing on cell-type-specific patterns of promoters and enhancers, we define multicell activity profiles for chromatin state, gene expression, regulatory motif enrichment and regulator expression. We use correlations between these profiles to link enhancers to putative target genes, and predict the cell-type-specific activators and repressors that modulate them. The resulting annotations and regulatory predictions have implications for the interpretation of genome-wide association studies. Top-scoring disease single nucleotide polymorphisms are frequently positioned within enhancer elements specifically active in relevant cell types, and in some cases affect a motif instance for a predicted regulator, thus suggesting a mechanism for the association. Our study presents a general framework for deciphering cis-regulatory connections and their roles in disease.
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?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“To some degree this can be overcome by correlative approaches (e.g. correlating open chromatin status between promoters and enhancers across large numbers of cell types) but such links remain inferential45,134,135.”
From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [135]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Currently mono-methylation of histone H3 lysine 4 (H3K4me1), associated with the binding of Trithorax/MLL complexes, is taken to be the hallmark of both ‘primed’ and active enhancers, whilst active enhancers additionally tend to associate with the acetylation of histone H3 lysine 27 (H3K27ac) [133–137].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [134]
Experimental — accuracy not yet measuredIn the citing paper
“ChIPseq using antibodies to H3K4Me3, a mark associated with active promoter sites (Ernst et al., 2011), and to H3K27Ac, a mark associated with enhancer elements (Heintzman et al., 2009), demonstrated mapped read peaks corresponding to at least four major transcriptional start sites within the SYNE1 locus (P1–P4), one of which (P3) lies immediately upstream of the p.L3206M mutation (Figure 3E).”
From Using Whole-Exome Sequencing to Identify Inherited Causes of Autism (2013) · cites this paper as Ernst et al., 2011
In the citing paper
“This mystery, which we will call the enhancer-gene specificity conundrum, is important to solve because the majority of disease-associated non-coding variation occurs in the vicinity of enhancers and thus likely impacts these enhancers’ target genes (Ernst et al., 2011; Farh et al., 2015; Hnisz et al., 2013; Maurano et al., 2012).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Ernst et al., 2011
In the citing paper
“Tens of thousands of non-coding genetic variants have been linked with various human diseases and traits in genome-wide association studies (GWAS), and the majority of these variants occur in enhancers (Ernst et al., 2011; Farh et al., 2015; Hnisz et al., 2013; Maurano et al., 2012).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Ernst et al., 2011
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
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845
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 ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
Self-citationPruitt, K. D., Tatusova, T. A., & Maglott, D. R. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl842 · Cited by 4,441
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129
Self-citationHindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., & Manolio, T. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903103106 · Cited by 4,013
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971 · cited 1×
“We used annotations obtained through the UCSC Genome Browser 54 for RefSeq TSSs and transcribed regions 55 , PhastCons 56 , DNase-seq for K562 cells 12 , c-Myc ChIP-seq for K562 cells 13 , NF-κ B ChIP-seq for GM12878 14 , Oct4 in ES cells 24 and nuclear lamina 15 .”
Biological, clinical and population relevance of 95 loci for blood lipids
Teslovich, T. M., Musunuru, K., Smith, A. V., Edmondson, A. C., Stylianou, I. M., Koseki, M., Pirruccello, J. P., Ripatti, S., Chasman, D. I., Willer, C. J., et al. (2010) · Nature · doi:10.1038/nature09270 · Cited by 3,487
Flagged first, then by citations
1 of the 67 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Items 701–800 of 1,013
Zerbino, D. R., Johnson, N., Juettemann, T., Sheppard, D., Wilder, S. P., Lavidas, I., Nuhn, M., Perry, E. H., Raffaillac-Desfosses, Q., Sobral, D., et al. (2016) · Database · doi:10.1093/database/bav119 · Cited by 76
The adjustable nucleosome: an epigenetic signaling module
Turner, B. M. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.04.003 · Cited by 75
Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation
Wang, J., Zhao, Y., Zhou, X., Hiebert, S. W., Liu, Q., & Shyr, Y. (2018) · BMC Genomics · doi:10.1186/s12864-018-5016-z · Cited by 77
Jia, W., Deshmukh, A. P., Mani, S. A., Jolly, M. K., & Levine, H. (2019) · Physical Biology · doi:10.1088/1478-3975/ab34df · Cited by 75
Epigenetic modifications are associated with inter-species gene expression variation in primates
Zhou, X., Cain, C. E., Myrthil, M., Lewellen, N., Michelini, K., Davenport, E., Stephens, M., Pritchard, J. K., & Gilad, Y. (2014) · Genome biology · doi:10.1186/s13059-014-0547-3 · Cited by 76
Super Enhancers in Cancers, Complex Disease, and Developmental Disorders
Niederriter, A. R., Varshney, A., Parker, S. C. J., & Martin, D. M. (2015) · Genes · doi:10.3390/genes6041183 · Cited by 75
A polymorphism in human MR1 is associated with mRNA expression and susceptibility to tuberculosis
Seshadri, C., Thuong, N. T. T., Mai, N. T. H., Bang, N. D., Chau, T. T. H., Lewinsohn, D. M., Thwaites, G. E., Dunstan, S. J., & Hawn, T. R. (2016) · Genes and Immunity · doi:10.1038/gene.2016.41 · Cited by 75
High-order chromatin structure and the epigenome in SAHFs
Chandra, T., & Narita, M. (2012) · Nucleus · doi:10.4161/nucl.23189 · Cited by 75
Strategies to discover regulatory circuits of the mammalian immune system
Amit, I., Regev, A., & Hacohen, N. (2011) · Nature reviews. Immunology · doi:10.1038/nri3109 · Cited by 74
Pike, J. W., Lee, S. M., & Meyer, M. B. (2014) · BoneKEy Reports · doi:10.1038/bonekey.2013.216 · Cited by 74
PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition
Durham, T., Libbrecht, M. W., Howbert, J. J., Bilmes, J., & Noble, W. S. (2018) · Nature Communications · doi:10.1038/s41467-018-03635-9 · Cited by 74
Self-citationChae, M., Danko, C. G., & Kraus, W. L. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0656-3 · Cited by 74
Integrating Early Life Experience, Gene Expression, Brain Development, and Emergent Phenotypes
Weaver, I. C. G. (2014) · Advances in genetics · doi:10.1016/b978-0-12-800222-3.00011-5 · Cited by 74
Kumar, V., Gutierrez‐Achury, J., Kanduri, K., de Almeida, R. C., Hrdličková, B., Zhernakova, D. V., Westra, H.-J., Karjalainen, J. M., Ricaño-Ponce, I., Li, Y., et al. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu453 · Cited by 74
Zhang, S., Zhou, B., Kang, Y., Cui, X., Liu, A., Deleris, A., Greenberg, M., Cui, X., Qiu, Q., Lu, F., et al. (2015) · Cell Discovery · doi:10.1038/celldisc.2015.3 · Cited by 74
Zheng, Y., Fornelli, L., Compton, P. D., Sharma, S., Canterbury, J., Mullen, C., Zabrouskov, V., Fellers, R. T., Thomas, P. M., Licht, J. D., et al. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.053819 · Cited by 73
One SNP at a Time: Moving beyond GWAS in Psoriasis
Ray-Jones, H. F., Eyre, S., Barton, A. C., & Warren, R. B. (2016) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2015.11.025 · Cited by 73
Mazrooei, P., Kron, K. J., Zhu, Y., Zhou, S., Grillo, G., Mehdi, T., Ahmed, M., Severson, T., Guilhamon, P., Armstrong, N. S., et al. (2019) · Cancer Cell · doi:10.1016/j.ccell.2019.10.005 · Cited by 73
Sex- and age-dependent DNA methylation at the 17q12-q21 locus associated with childhood asthma
Naumova, A. K., Tuwaijri, A. A., Morin, A., Vaillancout, V. T., Madore, A., Berlivet, S., Kohan‐Ghadr, H., Moussette, S., & Laprise, C. (2013) · Human Genetics · doi:10.1007/s00439-013-1298-z · Cited by 73
New basal cell carcinoma susceptibility loci
Stacey, S., Helgason, H., Gudjonsson, S. A., Þorleifsson, G., Zink, F., Sigurðsson, Á., Kehr, B., Guðmundsson, J., Sulem, P., Sigurgeirsson, B., et al. (2015) · Nature Communications · doi:10.1038/ncomms7825 · Cited by 73
Genetic Determinants for Gestational Diabetes Mellitus and Related Metabolic Traits in Mexican Women
Huerta-Chagoya, A., Vázquez-Cárdenas, P., Moreno-Macías, H., Tapia-Maruri, L., Rodríguez-Guillén, R., López-Vite, E., García-Escalante, G., Escobedo-Aguirre, F., Parra-Covarrubias, A., Cordero-Brieño, R., et al. (2015) · PLOS ONE · doi:10.1371/journal.pone.0126408 · Cited by 72
Identification and analysis of murine pancreatic islet enhancers
Tennant, B., Robertson, A. G., Kramer, M. M., Li, L., Zhang, X., Beach, M., Thiessen, N., Chiu, R., Mungall, K. L., Whiting, C. J., et al. (2012) · Diabetologia · doi:10.1007/s00125-012-2797-5 · Cited by 72
Self-citationGenetic variants near MLST8 and DHX57 affect the epigenetic age of the cerebellum
Lu, A. T.-H., Hannon, E. J., Levine, M. E., Hao, K., Crimmins, E. M., Lunnon, K., Kozlenkov, A., Mill, J. S., Dracheva, S. M., & Horvath, S. (2016) · Nature Communications · doi:10.1038/ncomms10561 · Cited by 72
NeuroD1 Dictates Tumor Cell Differentiation in Medulloblastoma
Cheng, Y. F., Liao, S., Xu, G., Hu, J., Guo, D., Du, F., Contreras, A. V., Cai, K. Q., Peri, S., Wang, Y., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107782 · Cited by 72
Kato, L. M., Begum, N. A., Burroughs, A. M., Doi, T., Kawai, J., Daub, C. O., Kawaguchi, T., Matsuda, F., Hayashizaki, Y., & Honjo, T. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120791109 · Cited by 72
Genetic and Epigenetic Regulation of Human lincRNA Gene Expression
Popadin, K. Y., Gutiérrez‐Arcelus, M., Dermitzakis, E. T., & Antonarakis, S. E. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.10.022 · Cited by 72
Environmental influence on Pristionchus pacificus mouth form through different culture methods
Werner, M. S., Sieriebriennikov, B., Loschko, T., Namdeo, S., Lenuzzi, M., Dardiry, M., Renahan, T., Sharma, D. R., & Sommer, R. J. (2017) · Scientific Reports · doi:10.1038/s41598-017-07455-7 · Cited by 72
Zilbauer, M., Rayner, T. F., Clark, C., Coffey, A. J., Joyce, C. J., Palta, P., Palotie, A. V., Lyons, P., & Smith, K. G. C. (2013) · Blood · doi:10.1182/blood-2013-05-503201 · Cited by 71
Weinstein, J. S., Lezon-Geyda, K., Maksimova, Y. D., Craft, S., Zhang, Y., Su, M. Y., Schulz, V., Craft, J. E., & Gallagher, P. G. (2014) · Blood · doi:10.1182/blood-2014-06-582700 · Cited by 71
Nakato, R., Itoh, T., & Shirahige, K. (2013) · Genes to Cells · doi:10.1111/gtc.12058 · Cited by 71
Smoking and Risk of Multiple Sclerosis
Briggs, F. B. S., Acuna, B., Shen, L., Ramsay, P. P., Quach, H., BERNSTEIN, A. L., Bellesis, K. H., Kockum, I. S., Hedström, A. K., Alfredsson, L. S., et al. (2014) · Epidemiology · doi:10.1097/ede.0000000000000089 · Cited by 71
Chidambaran, V., Zhang, X., Martin, L. J., Ding, L., Weirauch, M. T., Geisler, K. J., Stubbeman, B. L., Sadhasivam, S., & Ji, H. (2017) · Pharmacogenomics and Personalized Medicine · doi:10.2147/pgpm.s132691 · Cited by 71
Self-citationSungalee, S., Liu, Y., Lambuta, R. A., Katanayeva, N., Donaldson Collier, M., Tavernari, D., Roulland, S., Ciriello, G., & Oricchio, E. (2021) · Nature Genetics · doi:10.1038/s41588-021-00842-x · Cited by 70
Diminished nuclear RNA decay upon Salmonella infection upregulates antibacterial noncoding RNAs
Imamura, K., Takaya, A., Ishida, Y., Fukuoka, Y., Taya, T., Nakaki, R., Kakeda, M., Imamachi, N., Sato, A., Yamada, T., et al. (2018) · The EMBO Journal · doi:10.15252/embj.201797723 · Cited by 70
Xu, Y., Wang, Y., Luo, J., Zhao, W., & Zhou, X. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx870 · Cited by 70
Activation of Oncogenic Super-Enhancers Is Coupled with DNA Repair by RAD51
Hazan, I., Monin, J., Bouwman, B. A. M., Crosetto, N., & Aqeilan, R. I. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.09.001 · Cited by 70
Functional interpretation of non‐coding sequence variation: Concepts and challenges
Paul, D. S., Soranzo, N., & Beck, S. (2013) · BioEssays · doi:10.1002/bies.201300126 · Cited by 70
Long-range regulators of the lncRNAHOTAIRenhance its prognostic potential in breast cancer
Milevskiy, M. J. G., Al‐Ejeh, F., Saunus, J. M., Northwood, K. S., Bailey, P. J., Betts, J. A., Reed, A. E. M., Nephew, K. P., Stone, A. M., Gee, J. M. W., et al. (2016) · Human Molecular Genetics · doi:10.1093/hmg/ddw177 · Cited by 70
He, M., Huang, T.-S., Li, S., Hong, H.-C., Chen, Z. B., Martin, M., Zhou, X., Huang, H., Su, S., Zhang, J., et al. (2019) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.118.312301 · Cited by 70
Treviño, L. S., Dong, J., Kaushal, A., Katz, T. A., Jangid, R. K., Robertson, M. J., Grimm, S. L., Ambati, C. R., Putluri, V., Cox, A. R., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15847-z · Cited by 70
Benton, M. L., Talipineni, S. C., Kostka, D., & Capra, J. A. (2019) · BMC Genomics · doi:10.1186/s12864-019-5779-x · Cited by 70
T cell immunity as a tool for studying epigenetic regulation of cellular differentiation
Russ, B. E., Prier, J. E., Rao, S., & Turner, S. J. (2013) · Frontiers in Genetics · doi:10.3389/fgene.2013.00218 · Cited by 69
Hu, C. Y., Mohtat, D., Yu, Y., Ko, Y.-A., Shenoy, N. K., Bhattacharya, S., Izquierdo, M. C., Park, A. S. D., Giricz, O., Vallumsetla, N., et al. (2014) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-14-0494 · Cited by 69
Thibodeau, S. N., French, A. J., McDonnell, S. K., Cheville, J. C., Middha, S., Tillmans, L. S., Riska, S. M., Baheti, S., Larson, M. C., Fogarty, Z. C., et al. (2015) · Nature Communications · doi:10.1038/ncomms9653 · Cited by 69
Self-citationEvolution of Gene Regulation in Humans
Reilly, S. K., & Noonan, J. P. (2016) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090314-045935 · Cited by 66
Karol, S. E., Mattano, L. A., Yang, W., Maloney, K. W., Smith, C. J., Liu, C., Ramsey, L. B., Fernandez, C. A., Chang, T. Y., Neale, G. A. M., et al. (2015) · Blood · doi:10.1182/blood-2015-10-673848 · Cited by 69
Weaver, I. C. G., Korgan, A. C., Lee, K., Wheeler, R. V., Hundert, A. S., & Goguen, D. (2017) · Frontiers in Behavioral Neuroscience · doi:10.3389/fnbeh.2017.00041 · Cited by 69
Guhathakurta, S., Bok, E., Evangelista, B., & Kim, Y. (2017) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2017.04.004 · Cited by 69
Khanal, J., Tayara, H., & Chong, K. T. (2020) · IEEE Access · doi:10.1109/access.2020.2982666 · Cited by 69
Application of histone modification-specific interaction domains as an alternative to antibodiesPreprint
Kungulovski, G., Kycia, I., Tamas, R., Jurkowska, R. Z., Kudithipudi, S., Henry, C., Reinhardt, R., Labhart, P., & Jeltsch, A. (2014) · Genome Research · doi:10.1101/gr.170985.113 · Cited by 69
Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulationPreprint
Werner, M. S., Sieriebriennikov, B., Prabh, N., Loschko, T., Lanz, C., & Sommer, R. J. (2018) · Genome Research · doi:10.1101/gr.234872.118 · Cited by 69
Annotation of chromatin states in 66 complete mouse epigenomes during development
van der Velde, A., Fan, K., Tsuji, J., Moore, J. E., Purcaro, M. J., Pratt, H., & Weng, Z. (2021) · Communications Biology · doi:10.1038/s42003-021-01756-4 · Cited by 68
Genetic and epigenetic contribution to complex traits
Kilpinen, H., & Dermitzakis, E. T. (2012) · Human Molecular Genetics · doi:10.1093/hmg/dds383 · Cited by 68
SETD2 histone modifier loss in aggressive GI stromal tumours
Huang, K. K., McPherson, J. R., Tay, S. T., Das, K., Tan, I. B., Ng, C. C. Y., Chia, N., Zhang, S. L., Myint, S. S., Hu, L., et al. (2015) · Gut · doi:10.1136/gutjnl-2015-309482 · Cited by 68
Structural basis for LIN54 recognition of CHR elements in cell cycle-regulated promoters
Marceau, A. H., Felthousen, J. G., Goetsch, P. D., Iness, A. N., Lee, H., Tripathi, S. M., Strome, S., Litovchick, L., & Rubin, S. M. (2016) · Nature Communications · doi:10.1038/ncomms12301 · Cited by 68
Zhu, Y., Tazearslan, C., & Suh, Y. (2017) · Experimental Biology and Medicine · doi:10.1177/1535370217713750 · Cited by 68
Perone, Y., Farrugia, A. J., Rodríguez-Meira, A., Győrffy, B., Ion, C., Uggetti, A., Chronopoulos, A., Marrazzo, P., Faronato, M., Shousha, S., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09676-y · Cited by 68
Chelladurai, P., Kuenne, C. T., Bourgeois, A., Günther, S., Valasarajan, C., Cherian, A. V., Rottier, R. J., Romanet, C., Weigert, A., Boucherat, O., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abe5407 · Cited by 67
Progress and opportunities of foundation models in bioinformatics
Li, Q., Hu, Z., Wang, Y., Li, L., Fan, Y., King, I., Jia, G., Wang, S., Song, L., & Li, Y. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae548 · Cited by 72
Zheng, S. L., Henry, A., Cannie, D. E., Lee, M., Miller, D., McGurk, K. A., Bond, I., Xu, X. Y., Issa, H. G., Francis, C., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01952-y · Cited by 67
Chromatin and epigenetic determinants of estrogen receptor alpha (ESR1) signaling
Magnani, L., & Lupien, M. (2013) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2013.04.026 · Cited by 67
Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics
Aguilar, C. A., & Craighead, H. G. (2013) · Nature Nanotechnology · doi:10.1038/nnano.2013.195 · Cited by 67
Lindholm, M. E., Giacomello, S., Solnestam, B. W., Fischer, H., Huss, M., Kjellqvist, S., & Sundberg, C. J. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006294 · Cited by 67
Tan, J. Y., Smith, A., da Silva, M. F., Matthey-Doret, C., Rueedi, R., Sönmez, R., Ding, D., Kutalik, Z., Bergmann, S., & Marques, A. C. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.02.009 · Cited by 67
Histone methylation in DNA repair and clinical practice: new findings during the past 5-years
Wei, S., Li, C., Yin, Z., Wen, J., Meng, H., Xue, L., & Wang, J. (2018) · Journal of Cancer · doi:10.7150/jca.23427 · Cited by 67
Yen, A., & Kellis, M. (2015) · Nature Communications · doi:10.1038/ncomms8973 · Cited by 67
Self-citationHuman Genome Replication Proceeds through Four Chromatin States
Julienne, H., Zoufir, A., Audit, B., & Arnéodo, A. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003233 · Cited by 66
Li, Y., & Kellis, M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw627 · Cited by 66
Self-citationAppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States
Da, L., Liu, Y., Yang, J., Tian, T., She, J., Ma, X., Xu, W., & Su, Z. (2019) · Frontiers in Plant Science · doi:10.3389/fpls.2019.01333 · Cited by 66
(2021) · doi:10.1038/s43587-021-00063-1 · Cited by 66
Self-citationRetractedRoost, M. S., Slieker, R. C., Bialecka, M., van Iperen, L., Gomes Fernandes, M. M., He, N., Suchiman, H. E. D., Szuhai, K., Carlotti, F., de Koning, E. J. P., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01077-3 · Cited by 65
Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos
Gisselbrecht, S. S., Barrera, L. A., Porsch, M., Aboukhalil, A., Estep, P. W., Vedenko, A., Palagi, A., Kim, Y., Zhu, X., Busser, B. W., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2558 · Cited by 65
Applying CRISPR–Cas9 tools to identify and characterize transcriptional enhancers
Lopes, R., Korkmaz, G., & Agami, R. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.79 · Cited by 65
Liang, J., Li, G., Liao, J., Huang, Z., Wen, J., Wang, Y., Chen, Z., Cai, G., Xu, W., Ding, Z., et al. (2022) · Cell Death and Differentiation · doi:10.1038/s41418-022-00929-w · Cited by 65
Epigenome-Modifying Tools in Asthma
Brook, P., Perry, M. M., Adcock, I. M., & Durham, A. L. (2015) · Epigenomics · doi:10.2217/epi.15.53 · Cited by 65
A genome-wide association study of marginal zone lymphoma shows association to the HLA region
Vijai, J., Wang, Z., Berndt, S. I., Skibola, C. F., Slager, S. L., de Sanjosé, S., Melbye, M., Glimelius, B., Bracci, P. M., Conde, L., et al. (2015) · Nature Communications · doi:10.1038/ncomms6751 · Cited by 65
Fachel, Â. A., Tahira, A. C., Vilella-Arias, S. A., Maracaja‐Coutinho, V., Gimba, E. R. P., Vignal, G. M., de Campos, F. S., Reis, E. M. R., & Verjovski‐Almeida, S. (2013) · Molecular Cancer · doi:10.1186/1476-4598-12-140 · Cited by 65
A bipartite boundary element restricts UBE3A imprinting to mature neurons
Hsiao, J. S., Germain, N. D., Wilderman, A. S., Stoddard, C. E., Wojenski, L., Villafano, G. J., Core, L. J., Cotney, J. L., & Chamberlain, S. J. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1815279116 · Cited by 65
Du, M., Yuan, T., Schilter, K. F., Dittmar, R. L., Mackinnon, A. C., Huang, X., Tschannen, M., Worthey, E. A., Jacob, H. J., Xia, S., et al. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu426 · Cited by 64
Self-citationEpigenetics/Programming in the HPA Axis
Buschdorf, J. P., & Meaney, M. J. (2015) · Comprehensive physiology · doi:10.1002/cphy.c140027 · Cited by 64
Li, Y., Zhang, Y., Li, S., Lu, J., Chen, J., Wang, Y., Li, Y., Xu, J., & Li, X. (2015) · Scientific Reports · doi:10.1038/srep08790 · Cited by 64
Siggens, L., Cordeddu, L., Rönnerblad, M., Lennartsson, A., & Ekwall, K. (2015) · Epigenetics & Chromatin · doi:10.1186/1756-8935-8-4 · Cited by 64
Rondinelli, B., Schwerer, H., Antonini, E., Gaviraghi, M., Lupi, A., Frenquelli, M., Cittaro, D., Segalla, S., Lemaı̂tre, J.-M., & Tonon, G. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv090 · Cited by 64
High Risk Population Isolate Reveals Low Frequency Variants Predisposing to Intracranial Aneurysms
Kurki, M., Gaál, E. I., Kettunen, J., Lappalainen, T., Menelaou, A., Anttila, V., Hof, F. N. G. V. ’., zu Fraunberg, M. V. U., Helisalmi, S., Hiltunen, M. O., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004134 · Cited by 64
Identification of lamin B–regulated chromatin regions based on chromatin landscapes
Zheng, X., Kim, Y., & Zheng, Y. (2015) · Molecular Biology of the Cell · doi:10.1091/mbc.e15-04-0210 · Cited by 64
Tobiasson, M., Abdulkadir, H., Lennartsson, A., Katayama, S., Marabita, F., Paepe, A. D., Karimi, M., Krjutškov, K., Einarsdóttir, E., Grövdal, M., et al. (2017) · Oncotarget · doi:10.18632/oncotarget.15807 · Cited by 64
Jägle, S., Busch, H. S., Freihen, V., Beyes, S., Schrempp, M., Boerries, M., & Hecht, A. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1007109 · Cited by 64
Paauw, N. D., Lely, A. T., Joles, J. A., Franx, A., Nikkels, P. G. J., Mokrý, M., & van Rijn, B. B. (2018) · Clinical Epigenetics · doi:10.1186/s13148-018-0508-x · Cited by 64
Co-regulation of transcription by BRG1 and BRM, two mutually exclusive SWI/SNF ATPase subunits
Raab, J. R., Runge, J. S., Spear, C. C., & Magnuson, T. (2017) · Epigenetics & Chromatin · doi:10.1186/s13072-017-0167-8 · Cited by 64
MAnorm2 for quantitatively comparing groups of ChIP-seq samplesPreprint
Tu, S., Li, M., Tan, F., Chen, H., Xu, J., Waxman, D. J., Zhang, Y., & Shao, Z. (2020) · Genome Research · doi:10.1101/gr.262675.120 · Cited by 64
Hashimoto, K., Suzuki, A. M., Dos Santos, A., Desterke, C., Collino, A., Ghisletti, S., Braun, E., Bonetti, A., Fort, A., Qin, X.-Y., et al. (2015) · Genome Research · doi:10.1101/gr.191031.115 · Cited by 64
Functional characterization of enhancer evolution in the primate lineage
Klein, J. C., Keith, A., Agarwal, V., Durham, T., & Shendure, J. (2018) · Genome Biology · doi:10.1186/s13059-018-1473-6 · Cited by 63
Self-citationErceg, J., Saunders, T. E., Girardot, C., Devos, D. P., Hufnagel, L., & Furlong, E. E. M. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004060 · Cited by 63
A Network Model of the Molecular Organization of Chromatin in Drosophila
van Bemmel, J. G., Filion, G. J. P., Rosado, A., Talhout, W., de Haas, M., van Welsem, T., van Leeuwen, F., & van Steensel, B. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.040 · Cited by 63
Corradin, O., Cohen, A. J., Luppino, J. M., Bayles, I., Schumacher, F. R., & Scacheri, P. C. (2016) · Nature Genetics · doi:10.1038/ng.3674 · Cited by 63
Bidirectional transcription initiation marks accessible chromatin and is not specific to enhancers
Young, R. S., Kumar, Y., Bickmore, W. A., & Taylor, M. S. (2017) · Genome biology · doi:10.1186/s13059-017-1379-8 · Cited by 63
Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles
Sakaue, S., Weinand, K., Isaac, S., Dey, K. K., Jagadeesh, K. A., Kanai, M., Watts, G. F. M., Zhu, Z., Accelerating Medicines Partnership® RA/SLE Program and Network, Albrecht, J., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01682-1 · Cited by 65
Harth-Hertle, M. L., Scholz, B. A., Erhard, F., Glaser, L. V., Dölken, L., Zimmer, R., & Kempkes, B. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003638 · Cited by 62
Epigenetic aberrations in acute myeloid leukemia: Early key events during leukemogenesis
Eriksson, A., Lennartsson, A., & Lehmann, S. (2015) · Experimental Hematology · doi:10.1016/j.exphem.2015.05.009 · Cited by 62
The Yin and Yang of Chromatin Dynamics In Stem Cell Fate Selection
Adam, R. C., & Fuchs, E. V. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.11.002 · Cited by 62
Metadata
- Authors
- Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., Ku, M., Durham, T., Kellis, M., & Bernstein, B. E.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Kellis, Manolis
- ORCID
- Venue
- Nature
- Published
- 2011-03-23
- Volume
- 473
- Issue
- 7345
- Pages
- 43-49
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3088773
- OpenAlex
- W2117792884
- Cited by
- 2,898
- References
- 67
- Citations by year
- 2026: 47 · 2025: 62 · 2024: 109 · 2023: 130 · 2022: 141 · 2021: 179 · 2020: 203 · 2019: 191 · 2018: 216 · 2017: 237 · 2016: 237 · 2015: 306 · 2014: 260 · 2013: 287 · 2012: 225
- FWCI
- 108.00
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- eScholarship (California Digital Library) (submittedVersion)
- PubMed Central
- Funders
- Howard Hughes Medical Institute
- Broad Institute
- National Institutes of Health (5u54hg004570-04)
- National Human Genome Research Institute (RC1HG005334, U54-HG004570, R01HG004037)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- histone modifications, cell type-specific chromatin, enhancers, promoter, insulators, cis-regulatory elements, transcriptional activators and repressors, genome-wide association study, human cell types
- MeSH terms
- Binding Sites, Cell Line, Cell Physiological Phenomena, Cells, Cultured, Chromatin, Chromosome Mapping, Gene Expression Regulation, Humans, Promoter Regions, Genetic, Transcription Factors, Reproducibility of Results, Genome, Human, Cell Line, Tumor, Hep G2 Cells
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
