The accessible chromatin landscape of the human genome
Open accessAbstract
DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ∼2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. We connect ∼580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is organized with dozens to hundreds of co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predict cell-type-specific functional behaviours. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation. An extensive map of human DNase I hypersensitive sites, markers of regulatory DNA, in 125 diverse cell and tissue types is described; integration of this information with other ENCODE-generated data sets identifies new relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. This paper describes the first extensive map of human DNaseI hypersensitive sites — markers of regulatory DNA — in 125 diverse cell and tissue types. Integration of this information with other data sets generated by ENCODE (Encyclopedia of DNA Elements) identified new relationships between chromatin accessibility, transcription, DNA methylation and regulatory-factor occupancy patterns. Evolutionary-conservation analysis revealed signatures of recent functional constraint within DNaseI hypersensitive sites.
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
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?
Assisted loading events are coupled with increases in enhancer activity as measured by DNase hypersensitivity or H3K27 acetylation (H3K27ac).
“Assisted loading events are coupled with increases in enhancer activity as measured by DNase hypersensitivity or H3K27 acetylation (H3K27ac), two well-established markers for active enhancers38–40.”
From Synergistic gene expression during the acute phase response is characterized by transcription factor assisted loading (2017) · cites this paper as [40]
The Introduction (page unavailable) describes DNaseI hypersensitivity as characteristic of active regulatory elements, including enhancers, and the section on stereotyped chromatin accessibility links DHS patterns to enhancer activity. This supports DNase hypersensitivity as an enhancer marker, but the cited paper does not establish H3K27ac as a marker or examine assisted-loading events. (LLM, conf=0.85)
Experimental — accuracy not yet measuredThe number of enhancers in the human genome ranges from 400,000 to 1,000,000 according to recent estimates.
“According to recent estimates, the number of enhancers in the human genome ranges from 400,000 to 1,000,000 [22,23].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [23]
In “A genome-wide map of distal DHS-to-promoter connectivity” (page not supplied), the paper identifies 578,905 distal DHSs as candidate enhancers, a count within the cited range. It does not estimate the total number of human enhancers as 400,000–1,000,000; its count is specifically of candidate enhancers connected to promoters. (LLM, conf=0.85)
Experimental — accuracy not yet measuredCorrelative approaches can partially overcome this, but such links remain inferential.
“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 [45]
Most genetic variation contributing to common psychiatric disorders is not in protein-coding regions.
“most genetic variation that contributes to common psychiatric disorders is not in protein-coding regions”
From Defining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders (2019) · cites this paper as Thurman et al., 2012
Assays that combine enzymatic digestion with sequencing to measure chromatin accessibility give an integrated map of chromatin states covering many functional regulatory elements.
“Thus, methods that measure chromatin accessibility by combining sensitivity to enzymatic digestion with sequencing6–8 provide an integrated map of chromatin states that encompasses a diverse repertoire of functional regulatory elements2,5.”
From Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility (2019) · cites this paper as [2]
Active regulatory elements are typically nucleosome free and accessible to transcriptional machinery.
“Both classical observations5 and recent genome-wide efforts2 have shown that active regulatory elements are canonically nucleosome free and accessible to transcriptional machinery.”
From Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility (2019) · cites this paper as [2]
Chromatin accessibility from bulk ATAC-seq and DNase-seq and the aggregate chromatin accessibility across different single-cell technologies were highly correlated.
“We found that chromatin accessibility from bulk ATAC-seq8 and DNase-seq2 and the aggregate chromatin accessibility across the different single-cell technologies18,19,24,25 were highly correlated (Fig. 1c,d).”
From Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility (2019) · cites this paper as [2]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Landscape of transcription in human cells
Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. (2012) · Nature · doi:10.1038/nature11233 · Cited by 5,187 · see citing works
Self-citationGENCODE: The reference human genome annotation for The ENCODE Project
Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research · doi:10.1101/gr.135350.111 · Cited by 4,585 · see citing works
miRBase: tools for microRNA genomics
Griffiths‐Jones, S., Saini, H. K., van Dongen, S., & Enright, A. J. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm952 · Cited by 4,349 · see citing works
FIMO: scanning for occurrences of a given motif
Grant, C. E., Bailey, T. L., & Noble, W. S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr064 · Cited by 4,247 · see citing works
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · see citing works
Self-citationThe long-range interaction landscape of gene promoters
Sanyal, A., Lajoie, B. R., Jain, G., & Dekker, J. (2012) · Nature · doi:10.1038/nature11279 · Cited by 1,489 · see citing works
Self-citationHigh-Resolution Mapping and Characterization of Open Chromatin across the Genome
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 · see citing works
Self-citationAn Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells
Kim, J., Chu, J., Shen, X., Wang, J., & Orkin, S. H. (2008) · Cell · doi:10.1016/j.cell.2008.02.039 · Cited by 1,321 · see citing works
Schultz, D. C., Ayyanathan, K., Negorev, D., Maul, G. G., & Rauscher, F. J. (2002) · Genes & Development · doi:10.1101/gad.973302 · Cited by 1,313 · see citing works
NUCLEASE HYPERSENSITIVE SITES IN CHROMATIN
Gross, D. S., & Garrard, W. T. (1988) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.57.070188.001111 · Cited by 1,233 · see citing works
Li, G., Ruan, X., Auerbach, R. K., Sandhu, K. S., Zheng, M., Wang, P., Poh, H. M., Goh, Y., Lim, J., Zhang, J., et al. (2012) · Cell · doi:10.1016/j.cell.2011.12.014 · Cited by 1,232 · see citing works
Self-citationDostie, J., Richmond, T., Arnaout, R., Selzer, R. R., Lee, W. L., Honan, T., Rubio, E. D., Krumm, A., Lamb, J., Nusbaum, C., et al. (2006) · Genome Research · doi:10.1101/gr.5571506 · Cited by 1,182 · see citing works
Self-citationChromatin accessibility pre-determines glucocorticoid receptor binding patterns
John, S., Sabo, P. J., Thurman, R. E., Sung, M.-H., Biddie, S. C., Johnson, T. A., Hager, G. L., & Stamatoyannopoulos, J. A. (2011) · Nature Genetics · doi:10.1038/ng.759 · Cited by 954 · see citing works
Self-citationFarazi, T. A., Spitzer, J., Morozov, P. S., & Tuschl, T. (2010) · The Journal of Pathology · doi:10.1002/path.2806 · Cited by 892 · see citing works
An expansive human regulatory lexicon encoded in transcription factor footprints
Neph, S. J., Vierstra, J. D., Stergachis, A. B., Reynolds, A. P., Haugen, E., Vernot, B., Thurman, R. E., John, S., Sandstrom, R. S., Johnson, A., et al. (2012) · Nature · doi:10.1038/nature11212 · Cited by 746 · see citing works
Self-citationDynamic DNA methylation across diverse human cell lines and tissuesPreprint
Varley, K. E., Gertz, J., Bowling, K. M., Parker, S. L., Reddy, T. E., Pauli, F., Cross, M. K., Williams, B. A., Stamatoyannopoulos, J. A., Crawford, G. E., et al. (2013) · Genome Research · doi:10.1101/gr.147942.112 · Cited by 693 · see citing works
Self-citationInsulators: exploiting transcriptional and epigenetic mechanisms
Gaszner, M., & Felsenfeld, G. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1925 · Cited by 649 · see citing works
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
Hesselberth, J. R., Chen, X., Zhang, Z., Sabo, P. J., Sandstrom, R., Reynolds, A. P., Thurman, R. E., Neph, S., Kuehn, M. S., Noble, W. S., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1313 · Cited by 559 · see citing works
Self-citationSong, L., Zhang, Z., Grasfeder, L. L., Boyle, A. P., Giresi, P. G., Lee, B.-K., Sheffield, N. C., Gräf, S., Huss, M., Keefe, D., et al. (2011) · Genome Research · doi:10.1101/gr.121541.111 · Cited by 500 · see citing works
Self-citationDeterminants and dynamics of genome accessibility
Bell, O., Tiwari, V. K., Thomä, N. H., & Schübeler, D. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3017 · Cited by 457 · see citing works
DNA methylation represses transcription in vivo
Siegfried, Z., Eden, S., Mendelsohn, M., Feng, X., Tsuberi, B.-Z., & Cedar, H. (1999) · Nature Genetics · doi:10.1038/9727 · Cited by 354 · see citing works
Weisbrod, S., & Weintraub, H. M. (1979) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.76.2.630 · Cited by 336 · see citing works
Chromatin structure and gene expression.
Felsenfeld, G., Boyes, J., Chung, J., Clark, D. J., & Studitsky, V. M. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.18.9384 · Cited by 333 · see citing works
Animal Transcription Networks as Highly Connected, Quantitative Continua
Biggin, M. D. (2011) · Developmental Cell · doi:10.1016/j.devcel.2011.09.008 · Cited by 308 · see citing works
Locus control regions: coming of age at a decade plus
Li, Q., Harju, S., & Peterson, K. R. (1999) · Trends in Genetics · doi:10.1016/s0168-9525(99)01780-1 · Cited by 229 · see citing works
Genome-wide profiling of salt fractions maps physical properties of chromatinPreprint
Henikoff, S., Henikoff, J. G., Sakai, A., Loeb, G. B., & Ahmad, K. (2008) · Genome Research · doi:10.1101/gr.087619.108 · Cited by 227 · see citing works
Talbot, D., & Grosveld, F. G. (1991) · The EMBO Journal · doi:10.1002/j.1460-2075.1991.tb07659.x · Cited by 226 · see citing works
Transcription of the hypersensitive site HS2 enhancer in erythroid cells.
Tuan, D. Y. H., Kong, S., & Hu, K. Q. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.23.11219 · Cited by 196 · see citing works
Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs
O'Geen, H., Squazzo, S. L., Iyengar, S., Blahnik, K., Rinn, J. L., Chang, H. Y., Green, R., & Farnham, P. J. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030089 · Cited by 178 · see citing works
ZNF274 Recruits the Histone Methyltransferase SETDB1 to the 3′ Ends of ZNF Genes
Frietze, S. E., O’Geen, H., Blahnik, K. R., Jin, V. X., & Farnham, P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015082 · Cited by 166 · see citing works
Rapid empirical discovery of optimal peptides for targeted proteomics
Stergachis, A. B., MacLean, B., Lee, K., Stamatoyannopoulos, J. A., & MacCoss, M. J. (2011) · Nature Methods · doi:10.1038/nmeth.1770 · Cited by 110 · see citing works
Self-citationPersonal and population genomics of human regulatory variationPreprint
Vernot, B., Stergachis, A. B., Maurano, M. T., Vierstra, J. D., Neph, S. J., Thurman, R. E., Stamatoyannopoulos, J. A., & Akey, J. M. (2012) · Genome Research · doi:10.1101/gr.134890.111 · Cited by 105 · see citing works
Self-citationForsberg, E. C., Downs, K. M., & Bresnick, E. H. (2000) · Blood · doi:10.1182/blood.v96.1.334 · Cited by 100 · see citing works
Rasheed, Z. A., Saleem, A., Ravee, Y., et al. (2002) · Experimental Cell Research · doi:10.1006/excr.2002.5550 · Cited by 62 · see citing works
Reddy, P. M., Stamatoyannopoulos, G., Papayannopoulou, T., & Shen, C. K. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)37191-0 · Cited by 43 · see citing works
Self-citationc-Myb associates with PML in nuclear bodies in hematopoietic cells
Dahle, Ø., Bakke, O., & Gabrielsen, O. S. (2004) · Experimental Cell Research · doi:10.1016/j.yexcr.2004.03.014 · Cited by 22 · see citing works
Flagged first, then by citations
Research works printed but not linked: 2
- [14]Wang J Genome-wide mapping of the binding sites of 119 transcription factors Nature 2012 In Press
- [35]The_ENCODE_Consortium Integrative Analysis of the Human Genome Nature 2012 In Press
Cited by
Sorted by citations
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works
RNA-Guided Human Genome Engineering via Cas9
Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., & Church, G. M. (2013) · Science · doi:10.1126/science.1232033 · Cited by 9,210 · see citing works
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422 · see citing works
Integrative 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 · see citing works
“(7) Conserved non-coding GERP elements obtained by subtracting parts of the above mentioned GERP elements that overlap exons.”
BackgroundSelf-citationLandscape of transcription in human cells
Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. (2012) · Nature · doi:10.1038/nature11233 · Cited by 5,187 · see citing works
Self-citationMaster Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.035 · Cited by 4,143 · see citing works
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716 · see citing works
Self-citationSuper-enhancers in the control of cell identity and disease
Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., Hoke, H. A., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.09.053 · Cited by 3,662 · see citing works
CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes
Gilbert, L. A., Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., Torres, S. E., Stern-Ginossar, N., Brandman, O., Whitehead, E. H., Doudna, J. A., et al. (2013) · Cell · doi:10.1016/j.cell.2013.06.044 · Cited by 3,696 · see citing works
ATAC-seq: a method for assaying chromatin accessibility genome-wide
Buenrostro, J. D., Wu, B., Chang, H. Y., & Greenleaf, W. J. (2015) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb2129s109 · Cited by 3,289 · see citing works
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 · see citing works
An atlas of active enhancers across human cell types and tissues
The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550 · see citing works
Expanded encyclopaedias of DNA elements in the human and mouse genomes
The ENCODE Project Consortium, Abascal, F., Acosta, R., Addleman, N. J., Adrian, J., Afzal, V., Ai, R., Aken, B., Akiyama, J. A., Jammal, O. A., et al. (2020) · Nature · doi:10.1038/s41586-020-2493-4 · Cited by 2,378 · see citing works
Self-citationA comparative encyclopedia of DNA elements in the mouse genome
Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B. D., et al. (2014) · Nature · doi:10.1038/nature13992 · Cited by 1,781 · see citing works
Self-citationGlobal epigenomic reconfiguration during mammalian brain development
Lister, R., Mukamel, E. A., Nery, J. R., Urich, M., Puddifoot, C. A., Johnson, N. D., Lucero, J., Huang, Y., Dwork, A. J., Schultz, M. D., et al. (2013) · Science · doi:10.1126/science.1237905 · Cited by 1,830 · see citing works
Chromatin architecture reorganization during stem cell differentiation
Dixon, J. R., Jung, I., Selvaraj, S., Shen, Y., Antosiewicz-Bourget, J. E., Lee, A. Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., et al. (2015) · Nature · doi:10.1038/nature14222 · Cited by 1,646 · see citing works
Genome-wide association studies
Uffelmann, E., Huang, Q. Q., Munung, N. S., de Vries, J., Okada, Y., Martin, A. R., Martin, H. C., Lappalainen, T., & Posthuma, D. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-021-00056-9 · Cited by 1,849 · see citing works
Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity
Saeed, S., Quintin, J., Kerstens, H. H. D., Rao, N. A., Aghajanirefah, A., Matarese, F., Cheng, S.-C., Ratter, J., Berentsen, K., van der Ent, M. A., et al. (2014) · Science · doi:10.1126/science.1251086 · Cited by 1,761 · see citing works
Chromatin accessibility and the regulatory epigenome
Klemm, S. L., Shipony, Z., & Greenleaf, W. J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-018-0089-8 · Cited by 1,793 · see citing works
chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
Schep, A. N., Wu, B., Buenrostro, J. D., & Greenleaf, W. J. (2017) · Nature Methods · doi:10.1038/nmeth.4401 · Cited by 1,680 · see citing works
ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
Granja, J. M., Corces, M. R., Pierce, S. E., Bagdatli, S. T., Choudhry, H., Chang, H. Y., & Greenleaf, W. J. (2021) · Nature Genetics · doi:10.1038/s41588-021-00790-6 · Cited by 1,392 · see citing works
The long-range interaction landscape of gene promoters
Sanyal, A., Lajoie, B. R., Jain, G., & Dekker, J. (2012) · Nature · doi:10.1038/nature11279 · Cited by 1,489 · see citing works
Self-citationTranscriptional enhancers: from properties to genome-wide predictions
Shlyueva, D., Stampfel, G., & Stark, A. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3682 · Cited by 1,356 · see citing works
Genome-wide association analysis identifies 13 new risk loci for schizophrenia
Multicenter Genetic Studies of Schizophrenia Consortium, Ripke, S., Psychosis Endophenotypes International Consortium, Wellcome Trust Case Control Consortium 2, O'Dushlaine, C., Chambert, K., Moran, J. L., Kähler, A. K., Akterin, S., Bergen, S. E., et al. (2013) · Nature Genetics · doi:10.1038/ng.2742 · Cited by 1,496 · see citing works
Pidsley, R., Zotenko, E., Peters, T. J., Lawrence, M. G., Risbridger, G. P., Molloy, P., Van Djik, S., Muhlhausler, B., Stirzaker, C., & Clark, S. J. (2016) · Genome biology · doi:10.1186/s13059-016-1066-1 · Cited by 1,480 · see citing works
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
Cusanovich, D. A., Daza, R., Adey, A., Pliner, H. A., Christiansen, L., Gunderson, K. L., Steemers, F. J., Trapnell, C., & Shendure, J. (2015) · Science · doi:10.1126/science.aab1601 · Cited by 1,248 · see citing works
Charting a dynamic DNA methylation landscape of the human genome
Ziller, M. J., Gu, H., Müller, F., Donaghey, J., Tsai, L. T.-Y., Kohlbacher, O., De Jager, P. L., Rosen, E. D., Bennett, D. A., Bernstein, B. E., et al. (2013) · Nature · doi:10.1038/nature12433 · Cited by 1,357 · see citing works
A high-resolution map of the three-dimensional chromatin interactome in human cells
Jin, F., Li, Y., Dixon, J. R., Selvaraj, S., Ye, Z., Lee, A. Y., Yen, C.-A., Schmitt, A. D., Espinoza, C. A., & Ren, B. (2013) · Nature · doi:10.1038/nature12644 · Cited by 1,208 · see citing works
Genome Regulation by Polycomb and Trithorax: 70 Years and Counting
Schuettengruber, B., Bourbon, H.-M., Di Croce, L., & Cavalli, G. (2017) · Cell · doi:10.1016/j.cell.2017.08.002 · Cited by 1,094 · see citing works
Thakore, P. I., D'Ippolito, A. M., Song, L., Safi, A., Shivakumar, N. K., Kabadi, A. M., Reddy, T. E., Crawford, G. E., & Gersbach, C. A. (2015) · Nature Methods · doi:10.1038/nmeth.3630 · Cited by 1,012 · see citing works
Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data
Dekker, J., Marti-Renom, M. A., & Mirny, L. A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3454 · Cited by 1,068 · see citing works
Self-citationThe role of regulatory variation in complex traits and disease
Albert, F. W., & Kruglyak, L. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3891 · Cited by 1,047 · see citing works
The selection and function of cell type-specific enhancers
Heinz, S., Romanoski, C. E., Benner, C., & Glass, C. K. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3949 · Cited by 1,010 · see citing works
Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
Mifsud, B., Tavares-Cadete, F., Young, A. N., Sugar, R., Schoenfelder, S., Ferreira, L., Wingett, S. W., Andrews, S., Grey, W., Ewels, P. A., et al. (2015) · Nature Genetics · doi:10.1038/ng.3286 · Cited by 990 · see citing works
BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis
Canver, M. C., Smith, E. C., Sher, F., Pinello, L., Sanjana, N. E., Shalem, O., Chen, D. D., Schupp, P. G., Vinjamur, D. S., Garcia, S. P., et al. (2015) · Nature · doi:10.1038/nature15521 · Cited by 886 · see citing works
Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data
Pliner, H. A., Packer, J. S., McFaline-Figueroa, J. L., Cusanovich, D. A., Daza, R. M., Aghamirzaie, D., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.044 · Cited by 789 · see citing works
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
Cusanovich, D. A., Hill, A. J., Aghamirzaie, D., Daza, R. M., Pliner, H. A., Berletch, J. B., Filippova, G. N., Huang, X., Christiansen, L., DeWitt, W. S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.052 · Cited by 759 · see citing works
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 · see citing works
Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain
Mo, A., Mukamel, E. A., Davis, F. P., Luo, C., Henry, G. L., Picard, S., Urich, M. A., Nery, J. R., Sejnowski, T. J., Lister, R., et al. (2015) · Neuron · doi:10.1016/j.neuron.2015.05.018 · Cited by 739 · see citing works
An atlas of genetic influences on osteoporosis in humans and mice
23andMe Research Team, Morris, J. A., Kemp, J. P., Youlten, S. E., Laurent, L., Logan, J. G., Chai, R. C., Vulpescu, N. A., Forgetta, V., Kleinman, A., et al. (2019) · Nature Genetics · doi:10.1038/s41588-018-0302-x · Cited by 773 · see citing works
Self-citationSystematic mapping of functional enhancer–promoter connections with CRISPR interference
Fulco, C. P., Munschauer, M., Anyoha, R., Munson, G., Grossman, S. R., Perez, E. M., Kane, M., Cleary, B., Lander, E. S., & Engreitz, J. M. (2016) · Science · doi:10.1126/science.aag2445 · Cited by 643 · see citing works
Clark, S. J., Argelaguet, R., Kapourani, C.-A., Stubbs, T. M., Lee, H. J., Alda-Catalinas, C., Krueger, F., Sanguinetti, G., Kelsey, G., Marioni, J. C., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03149-4 · Cited by 657 · see citing works
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 · see citing works
A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia
Gröschel, S., Sanders, M. A., Hoogenboezem, R., de Wit, E., Bouwman, B. A. M., Erpelinck, C., van der Velden, V. H. J., Havermans, M., Avellino, R., van Lom, K., et al. (2014) · Cell · doi:10.1016/j.cell.2014.02.019 · Cited by 687 · see citing works
Kapusta, A., Kronenberg, Z., Lynch, V. J., Zhuo, X., Ramsay, L., Bourque, G., Yandell, M., & Feschotte, C. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003470 · Cited by 687 · see citing works
Bauer, D. E., Kamran, S. C., Lessard, S., Xu, J., Fujiwara, Y., Lin, C., Shao, Z., Canver, M. C., Smith, E. C., Pinello, L., et al. (2013) · Science · doi:10.1126/science.1242088 · Cited by 653 · see citing works
Self-citationKaikkonen, M. U., Spann, N. J., Heinz, S., Romanoski, C. E., Allison, K. A., Stender, J. D., Chun, H. B., Tough, D. F., Prinjha, R. K., Benner, C., et al. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.07.010 · Cited by 672 · see citing works
Widespread plasticity in CTCF occupancy linked to DNA methylation
Wang, H., Maurano, M. T., Qu, H., Varley, K. E., Gertz, J., Pauli, F., Lee, K., Canfield, T., Weaver, M., Sandstrom, R., et al. (2012) · Genome Research · doi:10.1101/gr.136101.111 · Cited by 588 · see citing works
“…factor binding sites appear to be generally depleted for DNA methylation (Mukhopadhyay et al. 2004; Lister et al. 2009; Thurman et al. 2012) and that binding sites recognized by certain sequence-specific factors have been associated with lack of methylation (Straussman…”
Self-citationChromosome conformation elucidates regulatory relationships in developing human brain
Won, H., de la Torre-Ubieta, L., Stein, J. L., Parikshak, N. N., Huang, J., Opland, C. K., Gandal, M. J., Sutton, G. J., Hormozdiari, F., Lu, D., et al. (2016) · Nature · doi:10.1038/nature19847 · Cited by 584 · see citing works
Measuring biological age using omics data
Rutledge, J., Oh, H., & Wyss-Coray, T. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00511-7 · Cited by 570 · see citing works
Cell-of-origin chromatin organization shapes the mutational landscape of cancer
Polak, P., Karlić, R., Koren, A., Thurman, R., Sandstrom, R., Lawrence, M. S., Reynolds, A., Rynes, E., Vlahoviček, K., Stamatoyannopoulos, J. A., et al. (2015) · Nature · doi:10.1038/nature14221 · Cited by 557 · see citing works
Self-citationPartitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases
Gusev, A., Lee, S. H., Trynka, G., Finucane, H., Vilhjálmsson, B. J., Xu, H., Zang, C., Ripke, S., Bulik-Sullivan, B., Stahl, E., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.10.004 · Cited by 544 · see citing works
Absence of a simple code: how transcription factors read the genome
Slattery, M., Zhou, T., Yang, L., Dantas Machado, A. C., Gordân, R., & Rohs, R. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.07.002 · Cited by 537 · see citing works
Genome-wide analysis of noncoding regulatory mutations in cancer
Weinhold, N., Jacobsen, A., Schultz, N., Sander, C., & Lee, W. (2014) · Nature Genetics · doi:10.1038/ng.3101 · Cited by 484 · see citing works
Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin
Whalen, S., Truty, R. M., & Pollard, K. S. (2016) · Nature Genetics · doi:10.1038/ng.3539 · Cited by 456 · see citing works
Topology of mammalian developmental enhancers and their regulatory landscapes
de Laat, W., & Duboule, D. (2013) · Nature · doi:10.1038/nature12753 · Cited by 521 · see citing works
Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility
Lareau, C. A., Duarte, F. M., Chew, J. G., Kartha, V. K., Burkett, Z. D., Kohlway, A. S., Pokholok, D., Aryee, M. J., Steemers, F. J., Lebofsky, R., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0147-6 · Cited by 444 · see citing works
Dynamic regulation of transcriptional states by chromatin and transcription factors
Voss, T. C., & Hager, G. L. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3623 · Cited by 504 · see citing works
Zerbino, D. R., Wilder, S. P., Johnson, N., Juettemann, T., & Flicek, P. R. (2015) · Genome Biology · doi:10.1186/s13059-015-0621-5 · Cited by 429 · see citing works
Defining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders
Sullivan, P. F., & Geschwind, D. H. (2019) · Cell · doi:10.1016/j.cell.2019.01.015 · Cited by 452 · see citing works
“From Variant to Gene Becausemost genetic variation that contributes to commonpsychiatric disorders is not in protein-coding regions, a crucial step in understanding disease mechanisms is pinpointing the genes impacted by risk variants (Thurman et al., 2012; Visel et al., 2009).”
BackgroundFoxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification
Samstein, R. M., Arvey, A., Josefowicz, S. Z., Peng, X., Reynolds, A., Sandstrom, R., Neph, S., Sabo, P., Kim, J. M., Liao, W., et al. (2012) · Cell · doi:10.1016/j.cell.2012.06.053 · Cited by 472 · see citing works
Self-citationKlann, T. S., Black, J. B., Chellappan, M., Safi, A., Song, L., Hilton, I. B., Crawford, G. E., Reddy, T. E., & Gersbach, C. A. (2017) · Nature Biotechnology · doi:10.1038/nbt.3853 · Cited by 447 · see citing works
Self-citationPassive and active DNA methylation and the interplay with genetic variation in gene regulation
Gutierrez-Arcelus, M., Lappalainen, T., Montgomery, S. B., Buil, A., Ongen, H., Yurovsky, A., Bryois, J., Giger, T., Romano, L., Planchon, A., et al. (2013) · eLife · doi:10.7554/elife.00523 · Cited by 440 · see citing works
Wagner, J. R., Busche, S., Ge, B., Kwan, T., Pastinen, T., & Blanchette, M. (2014) · Genome biology · doi:10.1186/gb-2014-15-2-r37 · Cited by 446 · see citing works
Functional implications of genome topology
Cavalli, G., & Misteli, T. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2474 · Cited by 415 · see citing works
Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells
Gifford, C. A., Ziller, M. J., Gu, H., Trapnell, C., Donaghey, J., Tsankov, A., Shalek, A. K., Kelley, D. R., Shishkin, A. A., Issner, R., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.037 · Cited by 435 · see citing works
Qi, T., Wu, Y., Zeng, J., Zhang, F., Xue, A., Jiang, L., Zhu, Z., Kemper, K., Yengo, L., Zheng, Z., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04558-1 · Cited by 427 · see citing works
Self-citationYAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers
Stein, C., Bardet, A. F., Roma, G., Bergling, S., Clay, I., Ruchti, A., Agarinis, C., Schmelzle, T., Bouwmeester, T., Schübeler, D., et al. (2015) · PLOS Genetics · doi:10.1371/journal.pgen.1005465 · Cited by 414 · see citing works
Genome-wide meta-analysis identifies new susceptibility loci for migraine
North American Brain Expression Consortium, Anttila, V., UK Brain Expression Consortium, the International Headache Genetics Consortium, Winsvold, B. S., Gormley, P., Kurth, T., Bettella, F., McMahon, G., Kallela, M., et al. (2013) · Nature Genetics · doi:10.1038/ng.2676 · Cited by 410 · see citing works
Relationship Between Methylome and Transcriptome in Patients With Nonalcoholic Fatty Liver Disease
Murphy, S. K., Yang, H., Moylan, C. A., Pang, H., Dellinger, A., Abdelmalek, M. F., Garrett, M. E., Ashley–Koch, A., Suzuki, A., Tillmann, H. L., et al. (2013) · Gastroenterology · doi:10.1053/j.gastro.2013.07.047 · Cited by 391 · see citing works
Preissl, S., Fang, R., Huang, H., Zhao, Y., Raviram, R., Gorkin, D. U., Zhang, Y., Sos, B. C., Afzal, V., Dickel, D. E., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0079-3 · Cited by 332 · see citing works
Towards a comprehensive catalogue of validated and target-linked human enhancers
Gasperini, M., Tome, J. M., & Shendure, J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-019-0209-0 · Cited by 396 · see citing works
Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain
Luo, C., Lancaster, M. A., Castanon, R., Nery, J. R., Knoblich, J. A., & Ecker, J. R. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.12.001 · Cited by 370 · see citing works
Global reference mapping of human transcription factor footprints
Vierstra, J., Lazar, J., Sandstrom, R., Halow, J., Lee, K., Bates, D., Diegel, M., Dunn, D., Neri, F., Haugen, E., et al. (2020) · Nature · doi:10.1038/s41586-020-2528-x · Cited by 386 · see citing works
Self-citationThe Spatial Organization of the Human Genome
Bickmore, W. A. (2013) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091212-153515 · Cited by 391 · see citing works
Genetic dissection of the α-globin super-enhancer in vivo
Hay, D., Hughes, J. R., Babbs, C., Davies, J. O. J., Graham, B. J., Hanssen, L. L. P., Kassouf, M. T., Oudelaar, A. M., Sharpe, J. A., Suciu, M. C., et al. (2016) · Nature Genetics · doi:10.1038/ng.3605 · Cited by 385 · see citing works
Mayer, A., di Iulio, J., Maleri, S., Eser, U., Vierstra, J., Reynolds, A., Sandstrom, R., Stamatoyannopoulos, J. A., & Churchman, L. S. (2015) · Cell · doi:10.1016/j.cell.2015.03.010 · Cited by 367 · see citing works
Self-citationCorradin, O., Saiakhova, A., Akhtar-Zaidi, B., Myeroff, L., Willis, J., Cowper-Sal·lari, R., Lupien, M., Markowitz, S., & Scacheri, P. C. (2014) · Genome Research · doi:10.1101/gr.164079.113 · Cited by 366 · see citing works
Heritability and genomics of gene expression in peripheral blood
Wright, F. A., Sullivan, P. F., Brooks, A. I., Zou, F., Sun, W., Xia, K., Madar, V., Jansen, R., Chung, W., Zhou, Y.-H., et al. (2014) · Nature Genetics · doi:10.1038/ng.2951 · Cited by 362 · see citing works
A compendium of promoter-centered long-range chromatin interactions in the human genome
Jung, I., Schmitt, A., Diao, Y., Lee, A. J., Liu, T., Yang, D., Tan, C., Eom, J., Chan, M., Chee, S., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0494-8 · Cited by 362 · see citing works
Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples
Jin, W., Tang, Q., Wan, M., Cui, K., Zhang, Y., Ren, G., Ni, B., Sklar, J., Przytycka, T. M., Childs, R., et al. (2015) · Nature · doi:10.1038/nature15740 · Cited by 332 · see citing works
HIPSCI Consortium, Alasoo, K., Rodrigues, J., Mukhopadhyay, S., Knights, A. J., Mann, A. L., Kundu, K., Hale, C., Dougan, G., & Gaffney, D. J. (2018) · Nature Genetics · doi:10.1038/s41588-018-0046-7 · Cited by 338 · see citing works
Index and biological spectrum of human DNase I hypersensitive sites
Meuleman, W., Muratov, A., Rynes, E., Halow, J., Lee, K., Bates, D., Diegel, M., Dunn, D., Neri, F., Teodosiadis, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2559-3 · Cited by 331 · see citing works
Self-citationQiao, Y., Giannopoulou, E. G., Chan, C. H., Park, S.-H., Gong, S., Chen, J., Hu, X., Elemento, O., & Ivashkiv, L. B. (2013) · Immunity · doi:10.1016/j.immuni.2013.08.009 · Cited by 330 · see citing works
Astrocytic abnormalities and global DNA methylation patterns in depression and suicide
Nagy, C., Suderman, M., Yang, J., Szyf, M., Mechawar, N., Ernst, C., & Turecki, G. (2015) · Molecular Psychiatry · doi:10.1038/mp.2014.21 · Cited by 301 · see citing works
Cordell, H. J., Han, Y., Mells, G. F., Li, Y., Hirschfield, G. M., Greene, C. S., Xie, G., Juran, B. D., Zhu, D., Qian, D. C., et al. (2015) · Nature Communications · doi:10.1038/ncomms9019 · Cited by 287 · see citing works
Woo, D., Falcone, G. J., Devan, W. J., Brown, W. M., Biffi, A., Howard, T. D., Anderson, C. D., Brouwers, H. B., Valant, V., Battey, T. W. K., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.02.012 · Cited by 290 · see citing works
Medulloblastomics revisited: biological and clinical insights from thousands of patients
Hovestadt, V., Ayrault, O., Swartling, F. J., Robinson, G. W., Pfister, S. M., & Northcott, P. A. (2020) · Nature Reviews Cancer · doi:10.1038/s41568-019-0223-8 · Cited by 271 · see citing works
Role of DNA Methylation in Modulating Transcription Factor Occupancy
Maurano, M. T., Wang, H., John, S., Shafer, A., Canfield, T., Lee, K., & Stamatoyannopoulos, J. A. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.07.024 · Cited by 281 · see citing works
Self-citationWILDS: A Benchmark of in-the-Wild Distribution Shifts
Koh, P. W., Sagawa, S., Marklund, H., Xie, S. M., Zhang, M., Balsubramani, A., Hu, W., Yasunaga, M., Phillips, R. L., Gao, I., et al. (2020) · arXiv · doi:10.48550/arxiv.2012.07421 · Cited by 518 · see citing works
Decoding enhancers using massively parallel reporter assays
Inoue, F., & Ahituv, N. (2015) · Genomics · doi:10.1016/j.ygeno.2015.06.005 · Cited by 272 · see citing works
Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells
Sabbagh, M. F., Heng, J. S., Luo, C., Castanon, R. G., Nery, J. R., Rattner, A., Goff, L. A., Ecker, J. R., & Nathans, J. (2018) · eLife · doi:10.7554/elife.36187 · Cited by 245 · see citing works
Rasmussen, K. D., Jia, G., Johansen, J. V., Pedersen, M. T., Rapin, N., Bagger, F. O., Porse, B. T., Bernard, O. A., Christensen, J., & Helin, K. (2015) · Genes & Development · doi:10.1101/gad.260174.115 · Cited by 270 · see citing works
Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation
Siersbæk, R., Madsen, J. G. S., Javierre, B. M., Nielsen, R., Bagge, E. K., Cairns, J., Wingett, S. W., Traynor, S., Spivakov, M., Fraser, P., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.04.010 · Cited by 243 · see citing works
Lagging-strand replication shapes the mutational landscape of the genome
Reijns, M. A. M., Kemp, H., Ding, J., Marion de Procé, S., Jackson, A. P., & Taylor, M. S. (2015) · Nature · doi:10.1038/nature14183 · Cited by 241 · see citing works
DNA methylation disruption reshapes the hematopoietic differentiation landscape
Izzo, F., Lee, S. C., Poran, A., Chaligne, R., Gaiti, F., Gross, B., Murali, R. R., Deochand, S. D., Ang, C., Jones, P. W., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0595-4 · Cited by 236 · see citing works
A polymorphism in IRF4 affects human pigmentation through a tyrosinase-dependent MITF/TFAP2A pathway
Praetorius, C., Grill, C., Stacey, S. N., Metcalf, A. M., Gorkin, D. U., Robinson, K. C., Van Otterloo, E., Kim, R. S. Q., Bergsteinsdottir, K., Ogmundsdottir, M. H., et al. (2013) · Cell · doi:10.1016/j.cell.2013.10.022 · Cited by 228 · see citing works
Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer
Guo, H., Ahmed, M., Zhang, F., Yao, C. Q., Li, S., Liang, Y., Hua, J., Soares, F., Sun, Y., Langstein, J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3637 · Cited by 226 · see citing works
Cas9-chromatin binding information enables more accurate CRISPR off-target prediction
Singh, R., Kuscu, C., Quinlan, A., Qi, Y., & Adli, M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv575 · Cited by 217 · see citing works
Ko, Y.-A., Mohtat, D., Suzuki, M., Park, A. S. D., Izquierdo, M. C., Han, S. Y., Kang, H. M., Si, H., Hostetter, T., Pullman, J. M., et al. (2013) · Genome Biology · doi:10.1186/gb-2013-14-10-r108 · Cited by 225 · see citing works
- Authors
- Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., Garg, K., John, S., Sandstrom, R., Bates, D., Boatman, L., Canfield, T. K., Diegel, M., Dunn, D., Ebersol, A. K., Frum, T., Giste, E., Johnson, A. K., Johnson, E. M., Kutyavin, T., Lajoie, B., Lee, B.-K., Lee, K., London, D., Lotakis, D., Neph, S., Neri, F., Nguyen, E. D., Qu, H., Reynolds, A. P., Roach, V., Safi, A., Sanchez, M. E., Sanyal, A., Shafer, A., Simon, J. M., Song, L., Vong, S., Weaver, M., Yan, Y., Zhang, Z., Zhang, Z., Lenhard, B., Tewari, M., Dorschner, M. O., Hansen, R. S., Navas, P. A., Stamatoyannopoulos, G., Iyer, V. R., Lieb, J. D., Sunyaev, S. R., Akey, J. M., Sabo, P. J., Kaul, R., Furey, T. S., Dekker, J., Crawford, G. E., & Stamatoyannopoulos, J. A.
- Affiliations
- University of Washington (US)
- Duke University (US)
- Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa (ZA)
- University of Massachusetts Chan Medical School (US)
- The University of Texas at Austin (US)
- Chinese Academy of Sciences (CN)
- University of North Carolina at Chapel Hill (US)
- University of Bergen (NO)
- Brigham and Women's Hospital (US)
- Corresponding author
- Stamatoyannopoulos, John A.
- ORCID
- Rynes, Eric
- Vierstra, Jeff
- Maurano, Matthew T.
- Haugen, Eric
- Sheffield, Nathan C.
- Stergachis, Andrew B.
- Vernot, Benjamin
- Garg, Kavita
- Sandstrom, Richard
- Bates, Daniel
- Frum, Tristan
- Lajoie, Bryan
- Lee, Bum-Kyu
- Lee, Kristen
- Lotakis, Dimitra
- Neph, Shane
- Qu, Hongzhu
- Reynolds, Alex P.
- Safi, Alexias
- Sanyal, Amartya
- Simon, Jeremy M.
- Song, Lingyun
- Zhang, Zhancheng
- Zhang, Zhuzhu
- Lenhard, Boris
- Tewari, Muneesh
- Iyer, Vishwanath R.
- Sunyaev, Shamil R.
- Akey, Joshua M.
- Sabo, Peter J.
- Kaul, Rajinder
- Furey, Terrence S.
- Dekker, Job
- Crawford, Gregory E.
- Stamatoyannopoulos, John A.
- Venue
- Nature
- Published
- 2012-09
- Volume
- 489
- Issue
- 7414
- Pages
- 75-82
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3721348
- OpenAlex
- W1964963969
- Cited by
- 2,679
- References
- 36
- Citations by year
- 2026: 81 · 2025: 97 · 2024: 119 · 2023: 140 · 2022: 170 · 2021: 218 · 2020: 192 · 2019: 199 · 2018: 227 · 2017: 238 · 2016: 238 · 2015: 247 · 2014: 242 · 2013: 235 · 2012: 31
- FWCI
- 96.99
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- UNC Libraries
- Funders
- National Science Foundation (HHSN261200800001E, DGE-0-718124, 0718124)
- Norges Forskningsråd
- National Institutes of Health (#HHSN261200800001E, 5u54hg004563-04, HG004563)
- National Institute of Mental Health (R01MH084676)
- National Human Genome Research Institute (U54‑HG004563, U54HG004592, HG004592, HG004563, R01HG003143)
- National Cancer Institute (HHSN261200800001E), P30CA016086)
- National Institute of General Medical Sciences (R01GM076036, GM076036)
- National Institute of Diabetes and Digestive and Kidney Diseases (F30DK095678)
- 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
- DNase I hypersensitive sites, chromatin accessibility, cis-regulatory elements, enhancers, promoter, insulators, silencers, locus control region, cell type-specific gene regulation, DNA methylation, transcription factor occupancy, evolutionary constraints, mutation rate, pluripotent cells, human diversity, ENCODE
- MeSH terms
- Chromatin, Deoxyribonuclease I, DNA, DNA-Binding Proteins, Encyclopedias as Topic, Humans, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid, Transcription Factors, Transcription, Genetic, Genome, Human, DNA Footprinting, Evolution, Molecular, DNA Methylation, Genomics, Transcription Initiation Site, Molecular Sequence Annotation, Mutation Rate
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
