Genomic views of distant-acting enhancers

Initial sequencing and analysis of the human genome

International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216 · see citing works

The sequence of the human genome

Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909 · see citing works

RNA-Seq: a revolutionary tool for transcriptomics

Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174 · see citing works

Initial sequencing and comparative analysis of the mouse genome

Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187 · see citing works

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 · see citing works

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223 · see citing works

Finishing the euchromatic sequence of the human genome

International Human Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03001 · Cited by 4,971 · see citing works

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 4,408 · cited 1× · see citing works

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 · see citing works

Capturing Chromosome Conformation

Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652 · see citing works

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

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 · cited 1× · see citing works

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927 · see citing works

VISTA: computational tools for comparative genomics

Frazer, K. A., Pachter, L. S., Poliakov, A., Rubin, E. M., & Dubchak, I. L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh458 · Cited by 2,791 · see citing works

Histone modifications at human enhancers reflect global cell-type-specific gene expression

Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature · doi:10.1038/nature07829 · Cited by 2,533 · see citing works

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

Chen, X., Han, X., Yuan, P., Fang, F., Huss, M., Vega, V. B., Wong, E., Orlov, Y. L., Zhang, W., Jiang, J., et al. (2008) · Cell · doi:10.1016/j.cell.2008.04.043 · Cited by 2,474 · see citing works

Initial sequence of the chimpanzee genome and comparison with the human genome

The Chimpanzee Sequencing and Analysis Consortium (2005) · Nature · doi:10.1038/nature04072 · Cited by 2,459 · see citing works

Combinatorial patterns of histone acetylations and methylations in the human genome

Wang, Z., Zang, C., Rosenfeld, J. A., Schones, D. E., Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Peng, W., Zhang, M. Q., et al. (2008) · Nature Genetics · doi:10.1038/ng.154 · Cited by 2,331 · see citing works

Sickle Cell Anemia, a Molecular Disease

Pauling, L., Itano, H. A., Singer, S. J., & Wells, I. C. (1949) · Science · doi:10.1126/science.110.2865.543 · Cited by 2,319 · see citing works

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 2,238 · see citing works

Human Gene Mutation Database (HGMD®): 2003 update

Stenson, P., Ball, E. V., Mort, M., Phillips, A. D., Shiel, J. A., Thomas, N., Abeysinghe, S. S., Krawczak, M., & Cooper, D. (2003) · Human Mutation · doi:10.1002/humu.10212 · Cited by 1,887 · see citing works

Genome-Wide Location and Function of DNA Binding Proteins

Ren, B., Robert, F., Wyrick, J. J., Aparicio, O. M., Jennings, E. G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N. M., Kanin, E. I., et al. (2000) · Science · doi:10.1126/science.290.5500.2306 · Cited by 1,768 · see citing works

Ultraconserved Elements in the Human Genome

Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W. J., Mattick, J. S., & Haussler, D. (2004) · Science · doi:10.1126/science.1098119 · Cited by 1,732 · see citing works

Expression of a β-globin gene is enhanced by remote SV40 DNA sequences

Banerji, J., Rusconi, S., & Schaffner, W. (1981) · Cell · doi:10.1016/0092-8674(81)90413-x · Cited by 1,724 · see citing works

The UCSC Genome Browser Database: update 2006

Hinrichs, A. S. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj144 · Cited by 1,646 · see citing works

ChIP-seq accurately predicts tissue-specific activity of enhancers

Visel, A., Blow, M. J., Li, Z., Zhang, T., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F., et al. (2009) · Nature · doi:10.1038/nature07730 · Cited by 1,639 · see citing works

A Common Variant on Chromosome 9p21 Affects the Risk of Myocardial Infarction

Helgadottir, A., Thorleifsson, G., Manolescu, A., Gretarsdottir, S., Blondal, T., Jonasdottir, A., Jonasdottir, A., Sigurdsson, A., Baker, A., Palsson, A., et al. (2007) · Science · doi:10.1126/science.1142842 · Cited by 1,594 · see citing works

Whole-Genome Shotgun Assembly and Analysis of the Genome of <i>Fugu rubripes</i>

Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.-M., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., et al. (2002) · Science · doi:10.1126/science.1072104 · Cited by 1,591 · see citing works

A Common Allele on Chromosome 9 Associated with Coronary Heart Disease

McPherson, R., Pertsemlidis, A., Kavaslar, N., Stewart, A., Roberts, R., Cox, D. R., Hinds, D. A., Pennacchio, L. A., Tybjaerg-Hansen, A., Folsom, A. R., et al. (2007) · Science · doi:10.1126/science.1142447 · Cited by 1,587 · see citing works

Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse

Bernstein, B., Kamal, M., Lindblad‐Toh, K., Bekiranov, S., Bailey, D. K., Huebert, D. J., McMahon, S., Karlsson, E. K., Kulbokas, E. J., Gingeras, T., et al. (2005) · Cell · doi:10.1016/j.cell.2005.01.001 · Cited by 1,509 · see citing works

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A., et al. (2007) · Nature Methods · doi:10.1038/nmeth1068 · Cited by 1,454 · see citing works

Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner

Blanchette, M., Kent, W. J., Riemer, C., Elnitski, L., Smit, A. F. A., Roskin, K. M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E. D., et al. (2004) · Genome Research · doi:10.1101/gr.1933104 · Cited by 1,452 · see citing works

Deletion of a DNA Polymerase β Gene Segment in T Cells Using Cell Type-Specific Gene Targeting

Gu, H., Marth, J. D., Orban, P. C., Mossmann, H., & Rajewsky, K. (1994) · Science · doi:10.1126/science.8016642 · Cited by 1,397 · see citing works

Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C)

Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B., & de Laat, W. (2006) · Nature Genetics · doi:10.1038/ng1896 · Cited by 1,386 · see citing works

Distribution and intensity of constraint in mammalian genomic sequence

Cooper, G. M., Stone, E. A., Asimenos, G., Green, E. D., Batzoglou, S., & Sidow, A. (2005) · Genome Research · doi:10.1101/gr.3577405 · Cited by 1,359 · see citing works

Transcription regulation and animal diversity

Levine, M., & Tjian, R. (2003) · Nature · doi:10.1038/nature01763 · Cited by 1,309 · see citing works

Human–Mouse Alignments with BLASTZPreprint

Schwartz, S., Kent, W. J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R. C., Haussler, D. H., & Miller, W. (2002) · Genome Research · doi:10.1101/gr.809403 · Cited by 1,231 · see citing works

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elementsPreprint

Dostie, 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

PipMaker—A Web Server for Aligning Two Genomic DNA SequencesPreprint

Schwartz, S., Zhang, Z., Frazer, K. A., Smit, A. F. A., Riemer, C., Bouck, J. B., Gibbs, R. A., Hardison, R. C., & Miller, W. (2000) · Genome Research · doi:10.1101/gr.10.4.577 · Cited by 1,165 · see citing works

In vivo enhancer analysis of human conserved non-coding sequences

Pennacchio, L. A., Ahituv, N., Moses, A. M., Prabhakar, S., Nobrega, M. A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K. D., et al. (2006) · Nature · doi:10.1038/nature05295 · Cited by 1,165 · see citing works

A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly

Lettice, L. A. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg180 · Cited by 1,164 · see citing works

A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome

Wei, C.-L., Wu, Q., Vega, V. B., Chiu, K. P., Ng, P., Zhang, T., Shahab, A., Yong, H. C., Fu, Y., Weng, Z., et al. (2006) · Cell · doi:10.1016/j.cell.2005.10.043 · Cited by 1,141 · see citing works

Myogenic and morphogenetic defects in the heart tubes of murine embryos lacking the homeo box gene Nkx2-5.Preprint

Lyons, I. G., Parsons, L. M., Hartley, L., Li, R., Andrews, J. E., Robb, L., & Harvey, R. P. (1995) · Genes & Development · doi:10.1101/gad.9.13.1654 · Cited by 1,129 · see citing works

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

Iyer, V. R., Horak, C. E., Scafe, C., Botstein, D., Snyder, M. P., & Brown, P. O. (2001) · Nature · doi:10.1038/35054095 · Cited by 1,084 · see citing works

Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

Ku, M., Koche, R. P., Rheinbay, E., Mendenhall, E. M., Endoh, M., Mikkelsen, T. S., Aiden, A. P., Nusbaum, C., Xie, X. S., Chi, A. S., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000242 · Cited by 996 · see citing works

Gene Mutations in Human Hæmoglobin: the Chemical Difference Between Normal and Sickle Cell Hæmoglobin

INGRAM, V. M. (1957) · Nature · doi:10.1038/180326a0 · Cited by 978 · see citing works

Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development

Woolfe, A., Goodson, M., Goode, D. K., Snell, P., McEwen, G. K., Vavouri, T., Smith, S. F., North, P., Callaway, H., Kelly, K., et al. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0030007 · Cited by 970 · see citing works

Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions

Zhao, Z., Tavoosidana, G., Sjölinder, M., Göndör, A., Mariano, P., Wang, S., Kanduri, C., Lezcano, M., Sandhu, K. S., Singh, U., et al. (2006) · Nature Genetics · doi:10.1038/ng1891 · Cited by 957 · see citing works

Transcriptional Regulatory Elements in the Human Genome

Maston, G. A., Evans, S. K., & Green, M. R. (2006) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.7.080505.115623 · Cited by 937 · cited 1× · see citing works

Mapping complex disease traits with global gene expression

Cookson, W., Liang, L., Abecasis, G., Moffatt, M., & Lathrop, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2537 · Cited by 849 · see citing works

Identification of a Coordinate Regulator of Interleukins 4, 13, and 5 by Cross-Species Sequence Comparisons

Loots, G. G., Locksley, R. M., Blankespoor, C. M., Wang, Z., Miller, W., Rubin, E. M., & Frazer, K. A. (2000) · Science · doi:10.1126/science.288.5463.136 · Cited by 783 · see citing works

Genomic Regulatory Systems: Development and Evolution

Davidson, E. H. (2005) · Thammasat University Digital Collections · Cited by 690 · see citing works

Long-range chromatin regulatory interactions in vivo

Carter, D., Chakalova, L., Osborne, C. S., Dai, Y.-F., & Fraser, P. (2002) · Nature Genetics · doi:10.1038/ng1051 · Cited by 663 · see citing works

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

Cuddapah, S., Jothi, R., Schones, D. E., Roh, T.-Y., Cui, K., & Zhao, K. (2009) · Genome Research · doi:10.1101/gr.082800.108 · Cited by 637 · see citing works

Mapping proteinDNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene

Solomon, M. J., Larsen, P. L., & Varshavsky, A. (1988) · Cell · doi:10.1016/s0092-8674(88)90469-2 · Cited by 633 · see citing works

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

Zhao, X. D., Han, X., Chew, J. L., Liu, J., Chiu, K. P., Choo, A. B. H., Orlov, Y. L., Sung, W.-K. K., Shahab, A., Kuznetsov, V. A., et al. (2007) · Cell stem cell · doi:10.1016/j.stem.2007.08.004 · Cited by 616 · see citing works

Scanning Human Gene Deserts for Long-Range Enhancers

Nobrega, M. A., Ovcharenko, I., Afzal, V., & Rubin, E. M. (2003) · Science · doi:10.1126/science.1088328 · Cited by 608 · see citing works

A Common Allele on Chromosome 9 Associated With Coronary Heart Disease

McPherson, R., Pertsemlidis, A., Kavaslar, N., Stewart, A. F. R., Roberts, R., Cox, D., Hinds, D. A., Pennacchio, L. A., Tybjærg‐Hansen, A., Folsom, A. R., et al. (2007) · Obstetrical & Gynecological Survey · doi:10.1097/01.ogx.0000279314.45442.bb · Cited by 524 · see citing works

Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome

Boffelli, D., McAuliffe, J., Ovcharenko, D., Lewis, K. D., Ovcharenko, I., Pachter, L., & Rubin, E. M. (2003) · Science · doi:10.1126/science.1081331 · Cited by 516 · see citing works

Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly

Lettice, L. A., Horikoshi, T., Heaney, S. J. H., van Baren, M. J., van der Linde, H. C., Breedveld, G. J., Joosse, M., Akarsu, N. A., Oostra, B. A., Endo, N., et al. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.112212199 · Cited by 458 · see citing works

A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease risk

Emison, E. S., McCallion, A. S., Kashuk, C., Bush, R. T., Grice, E. A., Lin, S., Portnoy, M. E., Cutler, D. J., Green, E. D., & Chakravarti, A. (2005) · Nature · doi:10.1038/nature03467 · Cited by 456 · see citing works

Genomic strategies to identify mammalian regulatory sequences

Pennacchio, L., & Rubin, E. (2001) · Nature reviews genetics · doi:10.1038/35052548 · Cited by 417 · see citing works

Elimination of a long-range cis-regulatory module causes complete loss of limb-specificShhexpression and truncation of the mouse limb

Sagai, T., Hosoya, M., Mizushina, Y., Tamura, M., & Shiroishi, T. (2005) · Development · doi:10.1242/dev.01613 · Cited by 379 · see citing works

Mef2cis a direct transcriptional target of ISL1 and GATA factors in the anterior heart field during mouse embryonic development

Dodou, E., Verzi, M. P., Anderson, J. P., Xu, S.-M., & Black, B. L. (2004) · Development · doi:10.1242/dev.01256 · Cited by 365 · see citing works

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analysesPreprint

Fullwood, M. J., Wei, C., Liu, E. T., & Ruan, Y. (2009) · Genome Research · doi:10.1101/gr.074906.107 · Cited by 363 · see citing works

Dynamic regulation of Pdx1 enhancers by Foxa1 and Foxa2 is essential for pancreas development.Preprint

Gao, N., Lelay, J., Vatamaniuk, M., Rieck, S., Friedman, J. R., & Kaestner, K. (2008) · Genes & Development · doi:10.1101/gad.1752608 · Cited by 338 · see citing works

Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes

Sandelin, A., Bailey, P. J., Bruce, S., Engström, P. G., Klos, J. M., Wasserman, W. W., Ericson, J., & Lenhard, B. (2004) · BMC Genomics · doi:10.1186/1471-2164-5-99 · Cited by 333 · see citing works

Inducible expression of an hsp68-lacZ hybrid gene in transgenic mice

Kothary, R., Clapoff, S., Darling, S. M., Perry, M. D., Moran, L. A., & Rossant, J. (1989) · Development · doi:10.1242/dev.105.4.707 · Cited by 323 · see citing works

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

Visel, A., Prabhakar, S., Akiyama, J. A., Shoukry, M., Lewis, K. D., Holt, A., Plajzer-Frick, I., Afzal, V., Rubin, E. M., & Pennacchio, L. A. (2008) · Nature Genetics · doi:10.1038/ng.2007.55 · Cited by 321 · see citing works

Deletion of Ultraconserved Elements Yields Viable Mice

Ahituv, N., Zhu, Y., Visel, A., Holt, A., Afzal, V., Pennacchio, L. A., & Rubin, E. M. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050234 · Cited by 319 · see citing works

Long Human–Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse GenomePreprint

Hardison, R. C., Oeltjen, J. C., & Miller, W. (1997) · Genome Research · doi:10.1101/gr.7.10.959 · Cited by 314 · see citing works

Suz12 binds to silenced regions of the genome in a cell-type-specific mannerPreprint

Squazzo, S. L., O’Geen, H., Komashko, V., Krig, S. R., Jin, V. X., Jang, S.-W., Margueron, R., Reinberg, D., Green, R., & Farnham, P. (2006) · Genome Research · doi:10.1101/gr.5306606 · Cited by 310 · see citing works

Segregation at three loci explains familial and population risk in Hirschsprung disease

Gabriel, S., Salomon, R., Pelet, A., Angrist, M. H., Amiel, J., Fornage, M., Attié‐Bitach, T., Olson, J. M., Hofstra, R. M. W., Buys, C. H. C. M., et al. (2002) · Nature Genetics · doi:10.1038/ng868 · Cited by 273 · see citing works

Chromosomal dynamics at the Shh locus: limb bud-specific differential regulation of competence and active transcription

Amano, T., Sagai, T., Tanabe, H., Mizushina, Y., Nakazawa, H., & Shiroishi, T. (2009) · Developmental Cell · doi:10.1016/j.devcel.2008.11.011 · Cited by 268 · see citing works

β-Globin gene inactivation by DNA translocation in γβ-thalassaemi

Kioussis, D., Vanin, E., deLange, T., Flavell, R. A., & Grosveld, F. G. (1983) · Nature · doi:10.1038/306662a0 · Cited by 264 · see citing works

Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes.

Aparicio, S. A. J. R., Morrison, A., Gould, A. P., Gilthorpe, J. D., Chaudhuri, C., Rigby, P. W. J., Krumlauf, R. K., & Brenner, S. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.5.1684 · Cited by 258 · see citing works

Tbx1 regulates fibroblast growth factors in the anterior heart field through a reinforcing autoregulatory loop involving forkhead transcription factors

Hu, T., Yamagishi, H., Maeda, J., McAnally, J., Yamagishi, C., & Srivastava, D. (2004) · Development · doi:10.1242/dev.01399 · Cited by 257 · see citing works

The enhanceosome

Panne, D. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.12.002 · Cited by 257 · see citing works

Comparative genomics at the vertebrate extremes

Boffelli, D., Nóbrega, M. A., & Rubin, E. M. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1350 · Cited by 256 · see citing works

The Genomic Record of Humankind's Evolutionary Roots

Goodman, M. (1999) · The American Journal of Human Genetics · doi:10.1086/302218 · Cited by 247 · see citing works

Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome

Xi, H. S., Shulha, H. P., Lin, J. M., Vales, T. R., Fu, Y., Bodine, D. M., McKay, R. D. G., Chenoweth, J. G., Tesar, P. J., Furey, T. S., et al. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030136 · Cited by 218 · see citing works

Megabase deletions of gene deserts result in viable mice

Nóbrega, M. A., Zhu, Y., Plajzer-Frick, I., Afzal, V., & Rubin, E. M. (2004) · Nature · doi:10.1038/nature03022 · Cited by 214 · see citing works

A human model for multigenic inheritance: Phenotypic expression in Hirschsprung disease requires both the RET gene and a new 9q31 locus

Gabriel, S., Pelet, A., Hofstra, R. M. W., Angrist, M. H., Salomon, R., Croaker, D., Buys, C. H. C. M., Lyonnet, S., & Chakravarti, A. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.1.268 · Cited by 209 · see citing works

A transgene containing lacZ inserted into the dystonia locus is expressed in neural tube

Kothary, R., Clapoff, S., Brown, A. M., Campbell, R., Peterson, A. C., & Rossant, J. (1988) · Nature · doi:10.1038/335435a0 · Cited by 205 · see citing works

Long-range chromosomal interactions and gene regulation

Miele, A., & Dekker, J. (2008) · Molecular BioSystems · doi:10.1039/b803580f · Cited by 198 · see citing works

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

Robertson, A. G., Bilenky, M., Tam, A., Zhao, Y., Zeng, T., Thiessen, N., Cezard, T., Fejes, A. P., Wederell, E. D., Cullum, R., et al. (2008) · Genome Research · doi:10.1101/gr.078519.108 · Cited by 182 · see citing works

Close sequence comparisons are sufficient to identify human cis -regulatory elementsPreprint

Prabhakar, S., Poulin, F., Shoukry, M. I., Afzal, V., Rubin, E. M., Couronne, O., & Pennacchio, L. A. (2006) · Genome Research · doi:10.1101/gr.4717506 · Cited by 177 · see citing works

Point mutations in a distant sonic hedgehog cis-regulator generate a variable regulatory output responsible for preaxial polydactyly

Lettice, L. A., Hill, A. E., Devenney, P. S., & Hill, R. E. (2007) · Human Molecular Genetics · doi:10.1093/hmg/ddm370 · Cited by 172 · see citing works

Genomic location analysis by ChIP‐Seq

Barski, A., & Zhao, K. (2009) · Journal of Cellular Biochemistry · doi:10.1002/jcb.22077 · Cited by 169 · see citing works

Analysis of vertebrate SCL loci identifies conserved enhancers

Göttgens, B., Barton, L. M., Gilbert, J. G. R., Bench, A. J., Sánchez, M. J., Bahn, S., Mistry, S., Grafham, D. V., McMurray, A. A., Vaudin, M., et al. (2000) · Nature Biotechnology · doi:10.1038/72635 · Cited by 167 · see citing works

Deletion of α-globin genes in haemoglobin-H disease demonstrates multiple α-globin structural loci

Kan, Y. W., Dozy, A. M., VARMUS, H. E., Taylor, J. M., Holland, J. P., Lie‐Injo, L. E., Ganesan, J., & Todd, D. (1975) · Nature · doi:10.1038/255255a0 · Cited by 163 · see citing works

GATA-1 binding sites mapped in the β-globin locus by using mammalian chIp-chip analysis

Horak, C. E., Mahajan, M. C., Luscombe, N. M., Gerstein, M., Weissman, S. M., & Snyder, M. P. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.052706999 · Cited by 154 · see citing works

Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing

Wederell, E. D., Bilenky, M., Cullum, R., Thiessen, N., Dagpinar, M., Delaney, A., Varhol, R., Zhao, Y., Zeng, T., Bernier, B., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn382 · Cited by 150 · see citing works

Two Distal Downstream Enhancers Direct Expression of the Human Apolipoprotein E Gene to Astrocytes in the Brain

Grehan, S., Tse, E., & Taylor, J. M. (2001) · The Journal of Neuroscience · doi:10.1523/jneurosci.21-03-00812.2001 · Cited by 138 · see citing works

A Single MEF2 Site Governs Desmin Transcription in Both Heart and Skeletal Muscle during Mouse Embryogenesis

Kuisk, I. R., Li, H., Tran, D., & Capetanaki, Y. (1996) · Developmental Biology · doi:10.1006/dbio.1996.0046 · Cited by 133 · see citing works

Cardiac-Specific Activity of an Nkx2–5 Enhancer Requires an Evolutionarily Conserved Smad Binding Site

Lien, C., McAnally, J., Richardson, J. A., & Olson, E. N. (2002) · Developmental Biology · doi:10.1006/dbio.2002.0603 · Cited by 130 · see citing works

Multiple tissue-specific elements control the apolipoprotein E/C-I gene locus in transgenic mice

Simonet, W. S., Bucay, N., Pitas, R. E., Lauer, S., & Taylor, J. M. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)31491-1 · Cited by 124 · see citing works

Direct Activation of a GATA6 Cardiac Enhancer by Nkx2.5: Evidence for a Reinforcing Regulatory Network of Nkx2.5 and GATA Transcription Factors in the Developing Heart

Molkentin, J. D., Antos, C. L., Mercer, B. M., Taigen, T. L., Miano, J. M., & Olson, E. N. (2000) · Developmental Biology · doi:10.1006/dbio.1999.9544 · Cited by 116 · see citing works

Identification of upstream regulatory regions in the heart-expressed homeobox gene Nkx2-5

Reecy, J. M., Li, X., Yamada, M., DeMayo, F. J., Newman, C. S., Harvey, R. P., & Schwartz, R. J. (1999) · Development · doi:10.1242/dev.126.4.839 · Cited by 115 · see citing works

Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2bPreprint

McGaughey, D. M., Vinton, R. M., Huynh, J. L., Al-Saif, A. M., Beer, M., & McCallion, A. S. (2007) · Genome Research · doi:10.1101/gr.6929408 · Cited by 113 · see citing works

Enhancer identification through comparative genomics

Visel, A., Bristow, J. D., & Pennacchio, L. A. (2007) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2006.12.014 · Cited by 112 · see citing works

Qualifying the relationship between sequence conservation and molecular functionPreprint

Cooper, G. M., & Brown, C. D. (2008) · Genome Research · doi:10.1101/gr.7205808 · Cited by 109 · see citing works

Regulation ofOtx2expression and its functions in mouse forebrain and midbrain

Kurokawa, D., Kiyonari, H., Nakayama, R., Kimura-Yoshida, C., Matsuo, I., & Aizawa, S. (2004) · Development · doi:10.1242/dev.01220 · Cited by 108 · see citing works

Chapter 13 Long‐Range Gene Control and Genetic Disease

Kleinjan, D. A., & Lettice, L. A. (2008) · Advances in genetics · doi:10.1016/s0065-2660(07)00013-2 · Cited by 92 · see citing works

Complex modular cis-acting elements regulate expression of the cardiac specifying homeobox gene Csx/Nkx2.5

Tanaka, M., Wechsler, S. B., Lee, I. W., Yamasaki, N., Lawitts, J. A., & Izumo, S. (1999) · Development · doi:10.1242/dev.126.7.1439 · Cited by 86 · see citing works

The silent carrier allele: β thalassemia without a mutation in the β-globin gene or its immediate flanking regions

Semenza, G. L., Delgrosso, K., Poncz, M., Malladi, P., Schwartz, E., & Surrey, S. (1984) · Cell · doi:10.1016/0092-8674(84)90197-1 · Cited by 85 · see citing works

A Novel Candidate Gene for Mouse and Human Preaxial Polydactyly with Altered Expression in Limbs of Hemimelic extra-toes Mutant Mice

Clark, R. M., Marker, P. C., & Kingsley, D. M. (2000) · Genomics · doi:10.1006/geno.2000.6225 · Cited by 82 · see citing works

A variant in the sonic hedgehog regulatory sequence (ZRS) is associated with triphalangeal thumb and deregulates expression in the developing limb

Furniss, D., Lettice, L. A., Taylor, I. B., Critchley, P. S., Giele, H. P., Hill, R. E., & Wilkie, A. O. M. (2008) · Human Molecular Genetics · doi:10.1093/hmg/ddn141 · Cited by 81 · see citing works

Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer

Grice, E. A., Rochelle, E. S., Green, E. D., Chakravarti, A., & McCallion, A. S. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi408 · Cited by 80 · see citing works

Regulation ofOtx2expression and its functions in mouse epiblast and anterior neuroectoderm

Kurokawa, D., Takasaki, N., Kiyonari, H., Nakayama, R., Kimura-Yoshida, C., Matsuo, I., & Aizawa, S. (2004) · Development · doi:10.1242/dev.01219 · Cited by 76 · see citing works

Comparative studies on mammalian Hoxc8 early enhancer sequence reveal a baleen whale-specific deletion of a cis-acting element

Shashikant, C. S., Kim, C. B., Borbély, M. A., Wang, W. C. H., & Ruddle, F. H. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.26.15446 · Cited by 64 · see citing works

Evolutionary Duplication of a Hepatic Control Region in the Human Apolipoprotein E Gene Locus

Allan, C. M., Walker, D. W., & Taylor, J. M. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.44.26278 · Cited by 64 · see citing works

A series of ENU-induced single-base substitutions in a long-range cis-element altering Sonic hedgehog expression in the developing mouse limb bud

Masuya, H., Sezutsu, H., Sakuraba, Y., Sagai, T., Hosoya, M., Kaneda, H., Miura, I., Kobayashi, K., Sumiyama, K., Shimizu, A., et al. (2007) · Genomics · doi:10.1016/j.ygeno.2006.09.005 · Cited by 64 · see citing works

Generation of conditionalMef2cloxP/loxP mice for temporal- and tissue-specific analyses

Vong, L., Ragusa, M. J., & Schwarz, J. J. (2005) · genesis · doi:10.1002/gene.20152 · Cited by 63 · see citing works

Functional autonomy of distant-acting human enhancers

Visel, A., Akiyama, J. A., Shoukry, M. I., Afzal, V., Rubin, E. M., & Pennacchio, L. A. (2009) · Genomics · doi:10.1016/j.ygeno.2009.02.002 · Cited by 63 · see citing works

Identification of specific crosslinked histones after treatment of chromatin with formaldehyde

Lente, F. V., Jackson, J. F., & Weintraub, H. (1975) · Cell · doi:10.1016/0092-8674(75)90090-2 · Cited by 63 · see citing works

The core enhancer is essential for proper timing of MyoD activation in limb buds and branchial arches

Chen, J. C. J., & Goldhamer, D. J. (2003) · Developmental Biology · doi:10.1016/j.ydbio.2003.09.018 · Cited by 56 · see citing works

Exploiting human-fish genome comparisons for deciphering gene regulation

Ahituv, N. (2004) · Human Molecular Genetics · doi:10.1093/hmg/ddh229 · Cited by 49 · see citing works

Two Pax2/5/8-binding sites in Engrailed2 are required for proper initiation of endogenous mid-hindbrain expression

Song, D. L., & Joyner, A. L. (2000) · Mechanisms of Development · doi:10.1016/s0925-4773(99)00242-7 · Cited by 40 · see citing works

Dcode.org anthology of comparative genomic tools

Loots, G. G., & Ovcharenko, I. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki355 · Cited by 35 · see citing works

Identification of a novel enhancer of brain expression near the apoE gene cluster by comparative genomics

Zheng, P., Pennacchio, L. A., Goff, W. L., Rubin, E. M., & Smith, J. D. (2003) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/j.bbaexp.2003.10.007 · Cited by 29 · see citing works

Deletion of the major GATA1 enhancer HS 1 does not affect eosinophil GATA1 expression and eosinophil differentiation

Guyot, B., Valverde-Garduño, V., Porcher, C., & Vyas, P. (2004) · Blood · doi:10.1182/blood-2004-01-0108 · Cited by 26 · see citing works

Histone H3K27ac separates active from poised enhancers and predicts developmental state

Creyghton, M. P., Cheng, A. W., Welstead, G. G., Kooistra, T., Carey, B. W., Steine, E. J., Hanna, J., Lodato, M. A., Frampton, G. M., Sharp, P. A., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016071107 · Cited by 4,302 · see citing works

Mapping and analysis of chromatin state dynamics in nine human cell types

Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature · doi:10.1038/nature09906 · Cited by 2,898 · see citing works

A unique chromatin signature uncovers early developmental enhancers in humans

Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233 · see citing works

Transcription factors: from enhancer binding to developmental control

Spitz, F., & Furlong, E. E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3207 · Cited by 2,227 · see citing works

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

Lupiáñez, D. G., Kraft, K., Heinrich, V., Krawitz, P., Brancati, F., Klopocki, E., Horn, D., Kayserili, H., Opitz, J. M., Laxova, R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.004 · Cited by 2,132 · see citing works

Cleft lip and palate: understanding genetic and environmental influences

Dixon, M. J., Marazita, M. L., Beaty, T. H., & Murray, J. C. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2933 · Cited by 1,987 · see citing works

A map of the cis-regulatory sequences in the mouse genome

Shen, Y., Yue, F., McCleary, D. F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V. V., et al. (2012) · Nature · doi:10.1038/nature11243 · Cited by 1,361 · see citing works

Transcriptional 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

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

Gandal, M. J., Zhang, P., Hadjimichael, E., Walker, R. L., Chen, C., Liu, S., Won, H., van Bakel, H., Varghese, M., Wang, Y., et al. (2018) · Science · doi:10.1126/science.aat8127 · Cited by 1,247 · see citing works

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

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

Charting histone modifications and the functional organization of mammalian genomes

Zhou, V. W., Goren, A., & Bernstein, B. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2905 · Cited by 1,147 · see citing works

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

Fulco, C. P., Nasser, J., Jones, T. R., Munson, G., Bergman, D. T., Subramanian, V., Grossman, S. R., Anyoha, R., Doughty, B. R., Patwardhan, T. A., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0538-0 · Cited by 1,111 · see citing works

Roles, Functions, and Mechanisms of Long Non-Coding RNAs in Cancer

Fang, Y., & Fullwood, M. J. (2016) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2015.09.006 · Cited by 1,068 · see citing works

Non‐coding RNAs: regulators of disease

Taft, R. J., Pang, K. C., Mercer, T. R., Dinger, M. E., & Mattick, J. S. (2009) · The Journal of Pathology · doi:10.1002/path.2638 · Cited by 1,056 · see citing works

Functional and Mechanistic Diversity of Distal Transcription Enhancers

Bulger, M., & Groudine, M. (2011) · Cell · doi:10.1016/j.cell.2011.01.024 · Cited by 803 · see citing works

Gene regulation by the act of long non-coding RNA transcription

Kornienko, A. E., Guenzl, P. M., Barlow, D. P., & Pauler, F. M. (2013) · BMC Biology · doi:10.1186/1741-7007-11-59 · Cited by 716 · see citing works

The role of 3D genome organization in development and cell differentiation

Zheng, H., & Xie, W. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0132-4 · Cited by 711 · see citing works

THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER

Rockman, M. V. (2011) · Evolution · doi:10.1111/j.1558-5646.2011.01486.x · Cited by 661 · see citing works

Enhancers: five essential questions

Pennacchio, L. A., Bickmore, W. A., Dean, A., Nóbrega, M. A., & Bejerano, G. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3458 · Cited by 584 · see citing works

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

Lenhard, B., Sandelin, A., & Carninci, P. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3163 · Cited by 513 · see citing works

Annotating non-coding regions of the genome.

Alexander, R. P., Fang, G., Rozowsky, J., Snyder, M., & Gerstein, M. B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2814 · Cited by 464 · 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

The PsychENCODE project

Akbarian, S., Liu, C., Knowles, J. A., Vaccarino, F. M., Farnham, P. J., Crawford, G. E., Jaffe, A. E., Pinto, D., Dracheva, S., Geschwind, D. H., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.4156 · Cited by 451 · see citing works

EWS-FLI1 Utilizes Divergent Chromatin Remodeling Mechanisms to Directly Activate or Repress Enhancer Elements in Ewing Sarcoma

Riggi, N., Knoechel, B., Gillespie, S. M., Rheinbay, E., Boulay, G., Suvà, M. L., Rossetti, N. E., Boonseng, W. E., Oksuz, O., Cook, E., et al. (2014) · Cancer Cell · doi:10.1016/j.ccell.2014.10.004 · Cited by 447 · see citing works

The MLL3/MLL4 Branches of the COMPASS Family Function as Major Histone H3K4 Monomethylases at Enhancers

Hu, D., Gao, X., Morgan, M. A., Herz, H.-M., Smith, E. R., & Shilatifard, A. (2013) · Molecular and Cellular Biology · doi:10.1128/mcb.01181-13 · Cited by 439 · see citing works

Principles for the post-GWAS functional characterization of cancer risk loci

Freedman, M. L., Monteiro, Á. N. A., Gayther, S. A., Coetzee, G. A., Risch, A., Plass, C., Casey, G., Biasi, M. D., Carlson, C., Duggan, D. J., et al. (2011) · Nature Genetics · doi:10.1038/ng.840 · Cited by 436 · see citing works

ChIP-Seq identification of weakly conserved heart enhancers

Blow, M. J., McCulley, D. J., Li, Z., Zhang, T., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F., et al. (2010) · Nature Genetics · doi:10.1038/ng.650 · Cited by 417 · see citing works

The 3D genome in transcriptional regulation and pluripotency

Gorkin, D. U., Leung, D., & Ren, B. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.05.017 · Cited by 391 · see citing works

Chromatin Higher-order Structure and Dynamics

Woodcock, C. L., & Ghosh, R. P. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000596 · Cited by 384 · see citing works

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits

Corradin, 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

An atlas of dynamic chromatin landscapes in mouse fetal development

Gorkin, D. U., Barozzi, I., Zhao, Y., Zhang, Y., Huang, H., Lee, A. Y., Li, B., Chiou, J., Wildberg, A., Ding, B., et al. (2020) · Nature · doi:10.1038/s41586-020-2093-3 · Cited by 364 · see citing works

Locus-specific editing of histone modifications at endogenous enhancers

Mendenhall, E. M., Williamson, K. E., Reyon, D., Zou, J., Ram, O., Joung, J. K., & Bernstein, B. (2013) · Nature Biotechnology · doi:10.1038/nbt.2701 · Cited by 362 · see citing works

Mechanisms of enhancer action: the known and the unknown

Panigrahi, A., & O’Malley, B. W. (2021) · Genome biology · doi:10.1186/s13059-021-02322-1 · Cited by 351 · see citing works

DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes

Aran, D., Sivan Sabato, A., & Hellman, A. (2013) · Genome biology · doi:10.1186/gb-2013-14-3-r21 · Cited by 335 · see citing works

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

Kieffer-Kwon, K.-R., Tang, Z., Mathé, E. A., Qian, J., Sung, M., Li, G., Resch, W., Baek, S., Pruett, N. D., Grøntved, L., et al. (2013) · Cell · doi:10.1016/j.cell.2013.11.039 · Cited by 326 · see citing works

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

Grubert, F., Zaugg, J. B., Kasowski, M., Ursu, O., Spacek, D. V., Martin, A. R., Greenside, P., Srivas, R., Phanstiel, D. H., Pekowska, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.048 · Cited by 319 · see citing works

Modulation of tissue repair by regeneration enhancer elements

Kang, J., Hu, J., Karra, R., Dickson, A. L., Tornini, V. A., Nachtrab, G. T., Gemberling, M. P., Goldman, J., Black, B. L., & Poss, K. D. (2016) · Nature · doi:10.1038/nature17644 · Cited by 315 · see citing works

Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer

Xiao, L., Parolia, A., Qiao, Y., Bawa, P., Eyunni, S., Mannan, R., Carson, S. E., Chang, Y., Wang, X., Zhang, Y., et al. (2021) · Nature · doi:10.1038/s41586-021-04246-z · Cited by 315 · see citing works

High-resolution interrogation of functional elements in the noncoding genome

Sanjana, N. E., Wright, J. B., Zheng, K., Shalem, O., Fontanillas, P., Joung, J., Cheng, C. S., Regev, A., & Zhang, F. (2016) · Science · doi:10.1126/science.aaf7613 · Cited by 280 · see citing works

Genetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms

Walker, R. L., Ramaswami, G., Hartl, C., Mancuso, N., Gandal, M. J., de la Torre-Ubieta, L., Paşaniuc, B., Stein, J. L., & Geschwind, D. H. (2019) · Cell · doi:10.1016/j.cell.2019.09.021 · Cited by 259 · see citing works

Direct lineage conversions: unnatural but useful?

Vierbuchen, T., & Wernig, M. (2011) · Nature Biotechnology · doi:10.1038/nbt.1946 · Cited by 259 · see citing works

Global view of enhancer–promoter interactome in human cells

He, B., Chen, C., Teng, L., & Tan, K. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1320308111 · Cited by 258 · see citing works

A High-Resolution Enhancer Atlas of the Developing Telencephalon

Visel, A., Taher, L., Girgis, H., May, D., Golonzhka, O., Hoch, R. V., McKinsey, G. L., Pattabiraman, K., Silberberg, S. N., Blow, M. J., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.041 · Cited by 257 · see citing works

Large-scale discovery of enhancers from human heart tissue

May, D., Blow, M. J., Kaplan, T., McCulley, D. J., Jensen, B. C., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M. I., Wright, C., et al. (2011) · Nature Genetics · doi:10.1038/ng.1006 · Cited by 256 · see citing works

Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus

Bell, C. G., Finer, S., Lindgren, C. M., Wilson, G. A., Rakyan, V. K., Teschendorff, A. E., Akan, P., Stupka, E., Down, T. A., Prokopenko, I., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0014040 · Cited by 255 · see citing works

Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo

Gilsbach, R., Schwaderer, M., Preißl, S., Grüning, B. A., Kranzhöfer, D., Schneider, P., Nührenberg, T. G., Mulero‐Navarro, S., Weichenhan, D., Braun, C., et al. (2018) · Nature Communications · doi:10.1038/s41467-017-02762-z · Cited by 248 · see citing works

Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing

Li, K., Liu, Y., Cao, H., Zhang, Y., Gu, Z., Liu, X., Yu, A., Kaphle, P., Dickerson, K. E., Ni, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14362-5 · Cited by 247 · see citing works

Coding exons function as tissue-specific enhancers of nearby genesPreprint

Birnbaum, R. Y., Clowney, E. J., Agamy, O., Kim, M. J., Zhao, J., Yamanaka, T., Pappalardo, Z., Clarke, S. L., Wenger, A. M., Nguyen, L., et al. (2012) · Genome Research · doi:10.1101/gr.133546.111 · Cited by 242 · see citing works

Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis

Huang, J., Liu, X., Li, D., Shao, Z., Cao, H., Zhang, Y., Trompouki, E., Bowman, T. V., Zon, L. I., Yuan, G., et al. (2016) · Developmental Cell · doi:10.1016/j.devcel.2015.12.014 · Cited by 239 · see citing works

Regulation of transcription in plants: mechanisms controlling developmental switches

Kaufmann, K., Pajoro, A., & Angenent, G. C. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2885 · Cited by 237 · see citing works

Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers

Attanasio, C., Nord, A. S., Zhu, Y., Blow, M. J., Li, Z., Liberton, D. K., Morrison, H., Plajzer-Frick, I., Holt, A., Hosseini, R., et al. (2013) · Science · doi:10.1126/science.1241006 · Cited by 237 · see citing works

Sex reversal following deletion of a single distal enhancer of <i>Sox9</i>

Gonen, N., Futtner, C. R., Wood, S., Garcia-Moreno, S. A., Salamone, I. M., Samson, S. C., Sekido, R., Poulat, F., Maatouk, D. M., & Lovell-Badge, R. (2018) · Science · doi:10.1126/science.aas9408 · Cited by 235 · see citing works

A histone acetylome-wide association study of Alzheimer’s disease identifies disease-associated H3K27ac differences in the entorhinal cortex

Marzi, S. J., Leung, S. K., Ribarska, T., Hannon, E., Smith, A. R., Pishva, E., Poschmann, J., Moore, K., Troakes, C., Al-Sarraj, S., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0253-7 · Cited by 232 · see citing works

Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancersPreprint

Sérandour, A. A., Avner, S., Percevault, F., Demay, F., Bizot, M., Lucchetti-Miganeh, C., Barloy-Hubler, F., Brown, M. A., Lupien, M., Métivier, R., et al. (2011) · Genome Research · doi:10.1101/gr.111534.110 · Cited by 228 · see citing works

Enhancer redundancy in development and disease

Kvon, E. Z., Waymack, R., Gad, M., & Wunderlich, Z. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00311-x · Cited by 227 · see citing works

The road to precision psychiatry: translating genetics into disease mechanisms

Gandal, M. J., Leppa, V., Won, H., Parikshak, N. N., & Geschwind, D. H. (2016) · Nature Neuroscience · doi:10.1038/nn.4409 · Cited by 223 · see citing works

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

Symmons, O., Pan, L., Remeseiro, S., Aktas, T., Klein, F., Huber, W., & Spitz, F. (2016) · Developmental Cell · doi:10.1016/j.devcel.2016.10.015 · Cited by 222 · see citing works

Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines

Cao, Q., Anyansi, C., Hu, X. S., Xu, L., Xiong, L., Tang, W., Mok, M. T. S., Cheng, C., Fan, X., Gerstein, M., et al. (2017) · Nature Genetics · doi:10.1038/ng.3950 · Cited by 216 · see citing works

In pursuit of design principles of regulatory sequences

Levo, M., & Segal, E. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3684 · Cited by 215 · see citing works

Advancing Personalized Medicine Through the Application of Whole Exome Sequencing and Big Data Analytics

Suwinski, P., Ong, C. K., Ling, M. H., Poh, Y. M., Khan, A. M., & Ong, H. S. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00049 · Cited by 213 · see citing works

Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease

Smemo, S., Campos, L. C. G., Moskowitz, I. P. G., Krieger, J. E., Pereira, A. C., & Nóbrega, M. A. (2012) · Human Molecular Genetics · doi:10.1093/hmg/dds165 · Cited by 201 · see citing works

Genetic Approaches to Neural Circuits in the Mouse

Josh Huang, Z., & Zeng, H. (2013) · Annual Review of Neuroscience · doi:10.1146/annurev-neuro-062012-170307 · Cited by 200 · see citing works

Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer

van den Boogaard, M., Wong, L. Y. E., Tessadori, F., Bakker, M. L., Dreizehnter, L., Wakker, V., Bezzina, C. R., Hoen, P. A. C. ’., Bakkers, J., Barnett, P., et al. (2012) · Journal of Clinical Investigation · doi:10.1172/jci62613 · Cited by 200 · see citing works

Mechanisms of specificity in neuronal activity-regulated gene transcription

Lyons, M. R., & West, A. E. (2011) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2011.05.003 · Cited by 199 · see citing works

An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancerPreprint

Wasserman, N. F., Aneas, I., & Nóbrega, M. A. (2010) · Genome Research · doi:10.1101/gr.105361.110 · Cited by 195 · see citing works

Distant eQTLs and Non-coding Sequences Play Critical Roles in Regulating Gene Expression and Quantitative Trait Variation in Maize

Liu, H., Luo, X., Niu, L., Xiao, Y., Chen, L., Liu, J., Wang, X., Jin, M., Li, W., Zhang, Q., et al. (2016) · Molecular Plant · doi:10.1016/j.molp.2016.06.016 · Cited by 193 · see citing works

Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm

Aksoy, I., Jauch, R., Chen, J., Dyla, M., Divakar, U., Bogu, G. K., Teo, R., Ng, C. K. L., Herath, W. B., Li-li, S., et al. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.31 · Cited by 192 · see citing works

Evolutionary conservation of the eumetazoan gene regulatory landscapePreprint

Schwaiger, M., Schönauer, A., Rendeiro, A. F., Pribitzer, C., Schauer, A., Gilles, A. F., Schinko, J. B., Renfer, E., Fredman, D., & Technau, U. (2014) · Genome Research · doi:10.1101/gr.162529.113 · Cited by 188 · see citing works

Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers

Sérandour, A. A., Avner, S., Oger, F., Bizot, M., Percevault, F., Lucchetti-Miganeh, C., Palierne, G., Gheeraert, C., Barloy-Hubler, F., Péron, C. L., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks595 · Cited by 186 · see citing works

Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains

Ron, G., Globerson, Y., Moran, D., & Kaplan, T. (2017) · Nature Communications · doi:10.1038/s41467-017-02386-3 · Cited by 182 · see citing works

Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics

Cooper, D. N., Chen, J., Ball, E. V., Howells, K., Mort, M. E., Phillips, A. D., Chuzhanova, N. A., Krawczak, M., Kehrer‐Sawatzki, H., & Stenson, P. D. (2010) · Human Mutation · doi:10.1002/humu.21260 · Cited by 181 · see citing works

Glioma Stem Cell–Specific Superenhancer Promotes Polyunsaturated Fatty-Acid Synthesis to Support EGFR Signaling

Gimple, R. C., Kidwell, R. L., Kim, L. J. Y., Sun, T., Gromovsky, A. D., Wu, Q., Wolf, M. E., Lv, D., Bhargava, S., Jiang, L., et al. (2019) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-0061 · Cited by 178 · see citing works

Cell-type-directed design of synthetic enhancers

Taskiran, I. I., Spanier, K. I., Dickmänken, H., Kempynck, N., Pančíková, A., Ekşi, E. C., Hulselmans, G., Ismail, J. N., Theunis, K., Vandepoel, R., et al. (2024) · Nature · doi:10.1038/s41586-023-06936-2 · Cited by 175 · see citing works

Identification of a chronic obstructive pulmonary disease genetic determinant that regulates HHIP

Zhou, X., Baron, R. M., Hardin, M. E., Cho, M. H., Zielinski, J., Hawryłkiewicz, I., Śliwiński, P., Hersh, C. P., Mancini, J. D., Lu, K., et al. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr569 · Cited by 173 · see citing works

Chromatin accessibility dynamics reveal novel functional enhancers in C. elegansPreprint

Daugherty, A. C., Yeo, R. W., Buenrostro, J. D., Greenleaf, W. J., Kundaje, A. B., & Brunet, A. (2017) · Genome Research · doi:10.1101/gr.226233.117 · Cited by 173 · see citing works

How far from the SNP may the causative genes be?

Brodie, A., Azaria, J. R., & Ofran, Y. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw500 · Cited by 172 · see citing works

Polycomb-Repressed Genes Have Permissive Enhancers that Initiate Reprogramming

Taberlay, P. C., Kelly, T. K., Liu, C.-C., You, J. S., Carvalho, D. D. D., Miranda, T. B., Zhou, X. J., Liang, G., & Jones, P. A. (2011) · Cell · doi:10.1016/j.cell.2011.10.040 · Cited by 172 · see citing works

Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function

Hawe, J. S., Wilson, R., Schmid, K., Zhou, L., Lakshmanan, L. N., Lehne, B. C., Kühnel, B., Scott, W. R., Wielscher, M., Yew, Y. W., et al. (2022) · Nature Genetics · doi:10.1038/s41588-021-00969-x · Cited by 167 · see citing works

LRP8-Reelin-regulated neuronal enhancer signature underlying learning and memory formation

Telese, F., Ma, Q., Perez, P. M., Notani, D., Oh, S., Li, W., Comoletti, D., Ohgi, K. A., Taylor, H., & Rosenfeld, M. G. (2015) · Neuron · doi:10.1016/j.neuron.2015.03.033 · Cited by 166 · see citing works

Direct observation of a condensate effect on super-enhancer controlled gene bursting

Du, M., Stitzinger, S. H., Spille, J.-H., Cho, W., Lee, C., Hijaz, M., Quintana, A., & Cissé, I. I. (2024) · Cell · doi:10.1016/j.cell.2023.12.005 · Cited by 165 · see citing works

Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants

Kvon, E. Z., Zhu, Y., Kelman, G., Novak, C. S., Plajzer-Frick, I., Kato, M., Garvin, T. H., Pham, Q. T., Harrington, A. N., Hunter, R. D., et al. (2020) · Cell · doi:10.1016/j.cell.2020.02.031 · Cited by 161 · see citing works

Identification of Functional Variants for Cleft Lip with or without Cleft Palate in or near PAX7, FGFR2, and NOG by Targeted Sequencing of GWAS Loci

Leslie, E. J., Taub, M. A., Liu, H., Steinberg, K. M., Koboldt, D. C., Zhang, Q., Carlson, J. C., Hetmanski, J. B., Wang, H., Larson, D. E., et al. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.01.004 · Cited by 160 · see citing works

Interleukin-4 Production by Follicular Helper T Cells Requires the Conserved Il4 Enhancer Hypersensitivity Site V

Vijayanand, P., Seumois, G., Simpson, L. J., Abdul‐Wajid, S., Baumjohann, D., Panduro, M., Huang, X., Interlandi, J., Djuretic, I. M., Brown, D. R., et al. (2012) · Immunity · doi:10.1016/j.immuni.2011.12.014 · Cited by 159 · see citing works

Genomics of Long-Range Regulatory Elements

Noonan, J. P., & McCallion, A. S. (2010) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082509-141651 · Cited by 159 · see citing works

Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor

Ruf, S., Symmons, O., Uslu, V. V., Dolle, D. D., Hot, C., Ettwiller, L. M., & Spitz, F. (2011) · Nature Genetics · doi:10.1038/ng.790 · Cited by 157 · see citing works

Integrating Diverse Datasets Improves Developmental Enhancer Prediction

Erwin, G. D., Oksenberg, N., Truty, R., Kostka, D., Murphy, K. K., Ahituv, N., Pollard, K. S., & Capra, J. A. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003677 · Cited by 154 · see citing works

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 152 · see citing works

Predicting enhancer transcription and activity from chromatin modifications

Zhu, Y. K., Sun, L., Zhao, C., Whitaker, J. W., Wang, T., & Wang, W. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt826 · Cited by 149 · see citing works

A unique H3K4me2 profile marks tissue-specific gene regulationPreprint

Pękowska, A., Benoukraf, T., Ferrier, P., & Spicuglia, S. (2010) · Genome Research · doi:10.1101/gr.109389.110 · Cited by 149 · see citing works

A Downstream Intergenic Cluster of Regulatory Enhancers Contributes to the Induction of CYP24A1 Expression by 1α,25-Dihydroxyvitamin D3

Meyer, M. B., Goetsch, P. D., & Pike, J. W. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.119958 · Cited by 147 · see citing works

Enhancer grammar in development, evolution, and disease: dependencies and interplay

Jindal, G. A., & Farley, E. K. (2021) · Developmental Cell · doi:10.1016/j.devcel.2021.02.016 · Cited by 147 · see citing works

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

Weirauch, M. T., & Hughes, T. R. (2010) · Trends in Genetics · doi:10.1016/j.tig.2009.12.002 · Cited by 146 · see citing works

Super-enhancer function and its application in cancer targeted therapy

Tang, F., Yang, Z., Tan, Y., & Li, Y. (2020) · npj Precision Oncology · doi:10.1038/s41698-020-0108-z · Cited by 143 · see citing works

Facial Genetics: A Brief Overview

Richmond, S., Howe, L. J., Lewis, S. J., Stergiakouli, E., & Zhurov, A. I. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00462 · Cited by 141 · see citing works

Transcriptional enhancers in development and disease

Sakabe, N. J., Savic, D., & Nóbrega, M. A. (2012) · Genome biology · doi:10.1186/gb-2012-13-1-238 · Cited by 138 · see citing works

BiRen: predicting enhancers with a deep-learning-based model using the DNA sequence alone

Yang, B., Liu, F., Ren, C., Ouyang, Z., Xie, Z., Bo, X., & Shu, W. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx105 · Cited by 136 · see citing works

Super-resolution microscopy compatible fluorescent probes reveal endogenous glucagon-like peptide-1 receptor distribution and dynamics

Ast, J., Arvaniti, A., Fine, N. H. F., Nasteska, D., Ashford, F. B., Stamataki, Z., Kőszegi, Z., Bacon, A., Jones, B. J., Lucey, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14309-w · Cited by 135 · see citing works

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis

Uslu, V. V., Petretich, M., Ruf, S., Langenfeld, K., Fonseca, N. A., Marioni, J. C., & Spitz, F. (2014) · Nature Genetics · doi:10.1038/ng.2971 · Cited by 133 · see citing works

Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance

Bi, M., Zhang, Z., Jiang, Y., Xue, P., Wang, H., Lai, Z., Fu, X., Angelis, C. D., Gong, Y., Gao, Z., et al. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-0514-z · Cited by 133 · see citing works

Regulatory Regions in DNA: Promoters, Enhancers, Silencers, and Insulators

Riethoven, J.-J. M. (2010) · Methods in molecular biology · doi:10.1007/978-1-60761-854-6_3 · Cited by 133 · see citing works

Distant‐acting Enhancers in Development and Disease

Visel, A. (2022) · The FASEB Journal · doi:10.1096/fasebj.2022.36.s1.0i627

The interaction between enhancer variants and environmental factors as an overlooked aetiological paradigm in human complex disease

Robert, S. M., & Rada-Iglesias, Á. (2023) · BioEssays · doi:10.1002/bies.202300038 · Cited by 1 · see citing works

Genome‐wide Analysis of Enhancers in Development and Disease

Ren, B. (2019) · The FASEB Journal · doi:10.1096/fasebj.2019.33.1_supplement.92.2

Blood disease–causing and –suppressing transcriptional enhancers: general principles and GATA2 mechanisms

Bresnick, E. H., & Johnson, K. D. (2019) · Blood Advances · doi:10.1182/bloodadvances.2019000378 · Cited by 32 · see citing works

Breaking enhancers to gain insights into developmental defects

Armendariz, D. A., Sundarrajan, A., & Hon, G. C. (2023) · eLife · doi:10.7554/elife.88187 · Cited by 9 · see citing works