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

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

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

Initial sequencing and comparative analysis of the mouse genome

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

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

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

Finishing the euchromatic sequence of the human genome

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

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

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971 · cited 1×

Capturing Chromosome Conformation

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

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×

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

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 2,821

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 2,547

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

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

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

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

Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells

Lee, T. I., Jenner, R. G., Boyer, L. A., Guenther, M. G., Levine, S. S., Kumar, R., Chevalier, B. S., Johnstone, S. E., Cole, M. F., Isono, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.043 · Cited by 2,296

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

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

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

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

The UCSC Genome Browser Database: update 2006

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

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

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

Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes

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

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

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 1,567

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

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

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

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

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

Transcription regulation and animal diversity

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

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 1,246

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 1,237

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

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

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

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

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

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

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 1,053

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

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

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

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×

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

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

Genomic Regulatory Systems: Development and Evolution

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

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

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. J. (1988) · Cell · doi:10.1016/s0092-8674(88)90469-2 · Cited by 650

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

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

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

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

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

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

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

Lettice, L., Horikoshi, T., Heaney, S., van Baren, M. V., van der Linde, H. C., Breedveld, G., Joosse, M., Akarsu, N., Oostra, B., Endo, N., et al. (2002) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.112212199 · Cited by 501

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

Genomic strategies to identify mammalian regulatory sequences

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

Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression 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 413

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 373

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

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

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 334

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 326

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 324

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 323

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 318

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

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

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

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

Comparative genomics at the vertebrate extremes

Boffelli, D., Nóbrega, M. A., & Rubin, E. M. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1350 · Cited by 259

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

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

The enhanceosome

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

The Genomic Record of Humankind's Evolutionary Roots

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

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 216

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. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0030136 · Cited by 215

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

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

Long-range chromosomal interactions and gene regulation

Miele, A., & Dekker, J. (2008) · Molecular BioSystems · doi:10.1039/b803580f · Cited by 200

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

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 179

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 176

Genomic location analysis by ChIP‐Seq

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

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

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

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 153

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

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

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

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 132

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

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

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

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 114

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 114

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 110

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

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., Taylor, I. B., Critchley, P., Giele, H., Hill, R., & Wilkie, A. (2008) · Human Molecular Genetics · doi:10.1093/hmg/ddn141 · Cited by 100

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 97

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

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

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

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 79

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 78

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 65

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

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

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

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

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

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

Exploiting human-fish genome comparisons for deciphering gene regulation

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

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

Dcode.org anthology of comparative genomic tools

Loots, G. G., & Ovcharenko, I. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki355 · Cited by 37

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

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

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

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

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

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

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

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

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

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