Transcriptional Regulatory Elements in the Human Genome

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

A haplotype map of the human genome

The International HapMap Consortium (2005) · Nature · doi:10.1038/nature04226 · Cited by 5,858

Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2

Amir, R. E., Van den Veyver, I. B., Wan, M., Tran, C. Q., Francke, U., & Zoghbi, H. Y. (1999) · Nature Genetics · doi:10.1038/13810 · Cited by 4,990

Finishing the euchromatic sequence of the human genome

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

Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells

Boyer, L. A., Lee, T. I., Cole, M. F., Johnstone, S. E., Levine, S. S., Zucker, J. P., Guenther, M. G., Kumar, R. M., Murray, H. L., Jenner, R. G., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.020 · Cited by 4,505

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 2×

Recurrent Fusion of TMPRSS2 and ETS Transcription Factor Genes in Prostate Cancer

Tomlins, S. A., Rhodes, D. R., Perner, S., Dhanasekaran, S. M., Mehra, R., Sun, X.-W., Varambally, S., Cao, X., Tchinda, J., Kuefer, R., et al. (2005) · Science · doi:10.1126/science.1117679 · Cited by 3,846

The immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome (IPEX) is caused by mutations of FOXP3

Bennett, C. L., Christie, J., Ramsdell, F., Brunkow, M., Ferguson, P., Whitesell, L., Kelly, T., Saulsbury, F., Chance, P., & Ochs, H. (2001) · Nature Genetics · doi:10.1038/83713 · Cited by 3,576

The Transcriptional Landscape of the Mammalian Genome

Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. A., et al. (2005) · Science · doi:10.1126/science.1112014 · Cited by 3,492

CpG Islands in vertebrate genomes

Gardiner‐Garden, M., & Frommer, M. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90689-9 · Cited by 3,417

Mutations in the DJ-1 Gene Associated with Autosomal Recessive Early-Onset Parkinsonism

Bonifati, V., Rizzu, P., van Baren, M. J., Schaap, O., Breedveld, G. J., Krieger, E., Dekker, M. C. J., Squitieri, F., Ibáñez, P., Joosse, M., et al. (2003) · Science · doi:10.1126/science.1077209 · Cited by 2,854

Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription

Jones, P. L., Veenstra, G. J. C., Wade, P. A., Vermaak, D., Kass, S. U., Landsberger, N., Strouboulis, J., & Wolffe, A. P. (1998) · Nature Genetics · doi:10.1038/561 · Cited by 2,791

Matlnd and Matlnspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data

Quandt, K., Frech, K., Karas, H., Wingender, E., & Werner, T. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.23.4878 · Cited by 2,587

Position-independent, high-level expression of the human β-globin gene in transgenic mice

Grosveld, F. G., van Assendelft, G. B., Greaves, D. R., & Kollias, G. A. (1987) · Cell · doi:10.1016/0092-8674(87)90584-8 · Cited by 1,908

Helix-Loop-Helix Proteins: Regulators of Transcription in Eucaryotic Organisms

Massari, M. E., & Murre, C. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.2.429-440.2000 · Cited by 1,848

JASPAR: an open-access database for eukaryotic transcription factor binding profiles

Sandelin, A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh012 · Cited by 1,804

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

Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene

Bell, A. C., & Felsenfeld, G. (2000) · Nature · doi:10.1038/35013100 · Cited by 1,746

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

Campomelic dysplasia and autosomal sex reversal caused by mutations in an SRY-related gene

Foster, J. W., Dominguez-Steglich, M., Guioli, S., Kwok, C., Weller, P., Stevanović, M., Weissenbach, J., Mansour, S., Young, I., Goodfellow, P., et al. (1994) · Nature · doi:10.1038/372525a0 · Cited by 1,602

Autosomal sex reversal and campomelic dysplasia are caused by mutations in and around the SRY-related gene SOX9.

Wagner, T., Wirth, J., Meyer, J., Zabel, B., Held, M., Zimmer, J., Pasantes, J., Bricarelli, F. D., Keutel, J., Hustert, E., et al. (1994) · Cell · doi:10.1016/0092-8674(94)90041-8 · Cited by 1,592

DNA binding sites: representation and discovery

Stormo, G. D. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.1.16 · Cited by 1,519

Transcription factors: structural families and principles of DNA recognition.

Pabo, C., & Sauer, R. (1992) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.61.070192.005201 · Cited by 1,445

A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes

Banerji, J., Olson, L., & Schaffner, W. (1983) · Cell · doi:10.1016/0092-8674(83)90015-6 · Cited by 1,381

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

Looping and Interaction between Hypersensitive Sites in the Active β-globin Locus

Tolhuis, B., Palstra, R.-J., Splinter, E., Grosveld, F., & de Laat, W. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00781-5 · Cited by 1,344

Congenital Heart Disease Caused by Mutations in the Transcription Factor NKX2-5

Schott, J., Benson, D. W., Basson, C. T., Pease, W., Silberbach, G. M., Moak, J. P., Maron, B. J., Seidman, C. E., & Seidman, J. G. (1998) · Science · doi:10.1126/science.281.5373.108 · Cited by 1,305

Assessing computational tools for the discovery of transcription factor binding sites

Tompa, M., Li, N., Bailey, T. L., Church, G. M., De Moor, B., Eskin, E., Favorov, A. V., Frith, M. C., Fu, Y., Kent, W. J., et al. (2005) · Nature Biotechnology · doi:10.1038/nbt1053 · Cited by 1,268

Transcriptional Control Signals of a Eukaryotic Protein-Coding Gene

McKnight, S. L., & Kingsbury, R. (1982) · Science · doi:10.1126/science.6283634 · Cited by 1,259

NUCLEASE HYPERSENSITIVE SITES IN CHROMATIN

Gross, D. S., & Garrard, W. T. (1988) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.57.070188.001111 · Cited by 1,233

The RNA Polymerase II Core Promoter

Smale, S. T., & Kadonaga, J. T. (2003) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.72.121801.161520 · Cited by 1,187

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

Transcriptional activation by recruitment

Ptashne, M., & Gann, A. (1997) · Nature · doi:10.1038/386569a0 · Cited by 1,158

The protein CTCF is required for the enhancer blocking activity of vertebrate insulators

Bell, A. C., West, A. G., & Felsenfeld, G. (1999) · Cell · doi:10.1016/s0092-8674(00)81967-4 · Cited by 1,101

Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs

Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., et al. (2004) · Cell · doi:10.1016/s0092-8674(04)00127-8 · Cited by 1,095

MATCHTM: a tool for searching transcription factor binding sites in DNA sequences

Kel, A. E. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg585 · Cited by 1,095

TRANSFAC: a database on transcription factors and their DNA binding sites

Wingender, E. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.1.238 · Cited by 1,064

The general transcription factors of RNA polymerase II.Preprint

Orphanides, G. M., Lagrange, T., & Reinberg, D. (1996) · Genes & Development · doi:10.1101/gad.10.21.2657 · Cited by 1,036

Virus induction of human IFNβ gene expression requires the assembly of an enhanceosome

Thanos, D., & Maniatis, T. (1995) · Cell · doi:10.1016/0092-8674(95)90136-1 · Cited by 1,014

Computational identification of Cis -regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae 1 1Edited by F. E. Cohen

Hughes, J. D., Estep, P. W., Tavazoie, S., & Church, G. M. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3519 · Cited by 1,008

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

TRANSCRIPTION OF EUKARYOTIC PROTEIN-CODING GENES

Lee, T. I., & Young, R. A. (2000) · Annual Review of Genetics · doi:10.1146/annurev.genet.34.1.77 · Cited by 889

Polyalanine expansion and frameshift mutations of the paired-like homeobox gene PHOX2B in congenital central hypoventilation syndrome

Amiel, J., Laudier, B., Attié‐Bitach, T., Trang, H., de Pontual, L., Gener, B., Trochet, D., Etchevers, H., Ray, P. F., Simonneau, M., et al. (2003) · Nature Genetics · doi:10.1038/ng1130 · Cited by 855

Going the Distance: A Current View of Enhancer Action

Blackwood, E. M., & Kadonaga, J. T. (1998) · Science · doi:10.1126/science.281.5373.60 · Cited by 836

Orchestrated response: a symphony of transcription factors for gene controlPreprint

Lemon, B. D., & Tjian, R. (2000) · Genes & Development · doi:10.1101/gad.831000 · Cited by 762

Interchromosomal associations between alternatively expressed loci

Spilianakis, C. G., Lalioti, M. D., Town, T., Lee, G. R., & Flavell, R. A. (2005) · Nature · doi:10.1038/nature03574 · Cited by 742

CpG islands as gene markers in the vertebrate nucleus

Bird, A. P. (1987) · Trends in Genetics · doi:10.1016/0168-9525(87)90294-0 · Cited by 678

The value of prior knowledge in discovering motifs with MEME.

Bailey, T. L., & Elkan, C. (1995) · PubMed · Cited by 665

Mutations in a putative global transcriptional regulator cause X-linked mental retardation with α-thalassemia (ATR-X syndrome)

Gibbons, R. J., Picketts, D. J., Villard, L., & Higgs, D. R. (1995) · Cell · doi:10.1016/0092-8674(95)90287-2 · Cited by 628

Insulators: many functions, many mechanismsPreprint

West, A. G., Gaszner, M., & Felsenfeld, G. (2002) · Genes & Development · doi:10.1101/gad.954702 · Cited by 624

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 Corepressor/Coactivator Exchange Complex Required for Transcriptional Activation by Nuclear Receptors and Other Regulated Transcription Factors

Perissi, V., Aggarwal, A. K., Glass, C. K., Rose, D. W., & Rosenfeld, M. G. (2004) · Cell · doi:10.1016/s0092-8674(04)00133-3 · Cited by 584

Evidence for stabilizing selection in a eukaryotic enhancer element

Ludwig, M. Z., Bergman, C., Patel, N. H., & Kreitman, M. (2000) · Nature · doi:10.1038/35000615 · Cited by 574

The human PAX6 gene is mutated in two patients with aniridia

Jordan, T., Hanson, I. M., Zaletaev, D. V., Hodgson, S. V., Prosser, J., Seawright, A., Hastie, N. D., & van Heyningen, V. (1992) · Nature Genetics · doi:10.1038/ng0892-328 · Cited by 572

Transcriptional coactivator complexes.

Näär, A. M., Lemon, B. D., & Tjian, R. (2001) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.70.1.475 · Cited by 571

Structure and mechanism of the RNA polymerase II transcription machinery

Hahn, S. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb763 · Cited by 546

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

Familial dyserythropoietic anaemia and thrombocytopenia due to an inherited mutation in GATA1

Nichols, K. E., Crispino, J. D., Poncz, M., White, J. G., Orkin, S. H., Maris, J. M., & Weiss, M. J. (2000) · Nature Genetics · doi:10.1038/73480 · Cited by 511

Allosteric effects of DNA on transcriptional regulators

Lefstin, J. A., & Yamamoto, K. R. (1998) · Nature · doi:10.1038/31860 · Cited by 489

Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Conservation and Turnover

Dermitzakis, E. T., & Clark, A. G. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004169 · Cited by 463

Locus control regions

Li, Q., Peterson, K. R., Fang, X., & Stamatoyannopoulos, G. (2002) · Blood · doi:10.1182/blood-2002-04-1104 · Cited by 456

Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease

Loots, G. G., Kneissel, M., Keller, H., Baptist, M., Chang, J., Collette, N. M., Ovcharenko, D., Plajzer-Frick, I., & Rubin, E. M. (2005) · Genome Research · doi:10.1101/gr.3437105 · Cited by 442

Association Between X-Linked Mixed Deafness and Mutations in the POU Domain Gene POU3F4

de Kok, Y. J. M., van der Maarel, S. M., Bitner-Glindzicz, M. A. K., Huber, I., Monaco, A. P., MALCOLM, S., Pembrey, M. E., Ropers, H., & Cremers, F. P. M. (1995) · Science · doi:10.1126/science.7839145 · Cited by 441

Non-coding RNAs: hope or hype?

Hüttenhofer, A., Schattner, P., & Polacek, N. (2005) · Trends in Genetics · doi:10.1016/j.tig.2005.03.007 · Cited by 437

Recruitment of CBP/p300 by the IFNβ Enhanceosome Is Required for Synergistic Activation of Transcription

Merika, M., Williams, A. J., Chen, G., Collins, T., & Thanos, D. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80028-3 · Cited by 435

Gene regulation by Sp1 and Sp3

Li, L., He, S., Sun, J., & Davie, J. (2004) · Biochemistry and Cell Biology · doi:10.1139/o04-045 · Cited by 418

Computational identification of promoters and first exons in the human genome

Davuluri, R. V., Große, I., & Zhang, M. Q. (2001) · Nature Genetics · doi:10.1038/ng780 · Cited by 414

Regulation of RNA Polymerase II Transcription by Sequence-Specific DNA Binding Factors

Kadonaga, J. T. (2004) · Cell · doi:10.1016/s0092-8674(03)01078-x · Cited by 403

Inappropriate Gene Activation in FSHD

Gabellini, D., Green, M. R., & Tupler, R. G. (2002) · Cell · doi:10.1016/s0092-8674(02)00826-7 · Cited by 401

One Nucleotide in a κB Site Can Determine Cofactor Specificity for NF-κB Dimers

Leung, T., Hoffmann, A., & Baltimore, D. (2004) · Cell · doi:10.1016/j.cell.2004.08.007 · Cited by 393

Use of Chromatin Immunoprecipitation To Clone Novel E2F Target Promoters

Weinmann, A. S., Bartley, S. M., Zhang, T., Zhang, M. Q., & Farnham, P. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.20.6820-6832.2001 · Cited by 383

Dynamic regulation of pol II transcription by the mammalian Mediator complex

Malik, S., & Roeder, R. G. (2005) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2005.03.009 · Cited by 382

Position-effect protection and enhancer blocking by the chicken β-globin insulator are separable activities

Targa, F. R., Pikaart, M. J., Burgess-Beusse, B. L., Bell, A. C., Litt, M. D., West, A. G., Gaszner, M., & Felsenfeld, G. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.102179399 · Cited by 381

Abundant Raw Material for Cis-Regulatory Evolution in Humans

Rockman, M. V., & Wray, G. A. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004023 · Cited by 378

Biological control through regulated transcriptional coactivators

Spiegelman, B. M., & Heinrich, R. (2004) · Cell · doi:10.1016/j.cell.2004.09.037 · Cited by 377

The xeroderma pigmentosum group D (XPD) gene: one gene, two functions, three diseasesPreprint

Lehmann, A. R. (2001) · Genes & Development · doi:10.1101/gad.859501 · Cited by 370

Embryonic ε and γ globin genes of a prosimian primate (Galago crassicaudatus)

Tagle, D. A., Koop, B. F., Goodman, M., Slightom, J. L., Hess, D. L., & Jones, R. T. (1988) · Journal of Molecular Biology · doi:10.1016/0022-2836(88)90011-3 · Cited by 363

A mechanism for synergistic activation of a mammalian gene by GAL4 derivatives

Carey, M., Lin, Y.-S., Green, M. R., & Ptashne, M. (1990) · Nature · doi:10.1038/345361a0 · Cited by 361

Dodecamer repeat expansion in cystatin B gene in progressive myoclonus epilepsy

Lalioti, M. D., Scott, H. S., Burési, C., Rossier, C., Bottani, A., Morris, M. A., Malafosse, A., & Antonarakis, S. E. (1997) · Nature · doi:10.1038/386847a0 · Cited by 353

Eukaryotic Promoter RecognitionPreprint

Fickett, J. W., & Hatzigeorgiou, A. G. (1997) · Genome Research · doi:10.1101/gr.7.9.861 · Cited by 342

The Role of Corepressors in Transcriptional Regulation by Nuclear Hormone Receptors

Privalsky, M. L. (2004) · Annual Review of Physiology · doi:10.1146/annurev.physiol.66.032802.155556 · Cited by 330

Binding affinities and cooperative interactions with bHLH activators delimit threshold responses to the dorsal gradient morphogen

Jiang, J. (1993) · Cell · doi:10.1016/0092-8674(93)90402-c · Cited by 327

Large-scale human promoter mapping using CpG islands

Ioshikhes, I. P., & Zhang, M. Q. (2000) · Nature Genetics · doi:10.1038/79189 · Cited by 312

Distribution of NF-κB-binding sites across human chromosome 22

Martone, R., Euskirchen, G. M., Bertone, P., Hartman, S. E., Royce, T. E., Luscombe, N. M., Rinn, J. L., Nelson, F. K., Miller, P. L., Gerstein, M., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2135255100 · Cited by 310

Remote control of gene transcription

West, A. G., & Fraser, P. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi104 · Cited by 302

Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes

Ogbourne, S. M., & Antalis, T. (1998) · Biochemical Journal · doi:10.1042/bj3310001 · Cited by 297

Computational Detection and Location of Transcription Start Sites in Mammalian Genomic DNAPreprint

Down, T. A., & Hubbard, T. (2002) · Genome Research · doi:10.1101/gr.216102 · Cited by 295

Mutation analysis of peroxisome proliferator-activated receptor-γ coactivator-1 (PGC-1) and relationships of identified amino acid polymorphisms to Type II diabetes mellitus

Ek, J., Andersen, G., Urhammer, S. A., Gæde, P. H., Drivsholm, T., Borch-Johnsen, K., Hansen, T., & Pedersen, O. (2001) · Diabetologia · doi:10.1007/s001250100032 · Cited by 293

The insulation of genes from external enhancers and silencing chromatin

Burgess-Beusse, B. L., Farrell, C. M., Gaszner, M., Litt, M. D., Mutskov, V. J., Targa, F. R., Simpson, M., West, A. G., & Felsenfeld, G. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.162342499 · Cited by 292

MyoD Targets Chromatin Remodeling Complexes to the Myogenin Locus Prior to Forming a Stable DNA-Bound Complex

de la Serna, I. L., Ohkawa, Y., Berkes, C. A., Bergstrom, D. A., Dacwag, C. S., Tapscott, S. J., & Imbalzano, A. N. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.10.3997-4009.2005 · Cited by 287

The Eukaryotic Promoter Database EPD

Périer, R. C. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.353 · Cited by 287

Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach

Scherf, M., Klingenhoff, A., & Werner, T. A. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3589 · Cited by 281

Combinatorial control of gene expression

Reményi, A., Schöler, H. R., & Wilmanns, M. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb820 · Cited by 280

Molecular Basis of Hereditary Persistence of Fetal Hemoglobin

Forget, B. G. (1998) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.1998.tb10460.x · Cited by 271

Transcriptional Regulation in Eukaryotes: Concepts, Strategies and Techniques

Carey, M., & Smale, S. T. (2000) · Cited by 253

Interleukin-10 and Transforming Growth Factor- β Promoter Polymorphisms in Allergies and Asthma

Hobbs, K., Negri, J. A., Klinnert, M. D., Rosenwasser, L. J., & Borish, L. (1998) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/ajrccm.158.6.9804011 · Cited by 251

Polyglutamine-expanded ataxin-7 inhibits STAGA histone acetyltransferase activity to produce retinal degeneration

Palhan, V. B., Chen, S., Peng, G.-H., Tjernberg, A., Gamper, A. M., Fan, Y., Chait, B. T., Spada, A. R. L., & Roeder, R. G. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0503505102 · Cited by 248

Functional analysis of human promoter polymorphisms

Hoogendoorn, B. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg246 · Cited by 247

How different eukaryotic transcriptional activators can cooperate promiscuously

Lin, Y.-S., Carey, M., Ptashne, M., & Green, M. R. (1990) · Nature · doi:10.1038/345359a0 · Cited by 245

Allosteric Effects of Pit-1 DNA Sites on Long-Term Repression in Cell Type Specification

Scully, K. M., Jacobson, E. M., Jepsen, K., Lunyak, V. V., Viadiu, H., Carrière, C., Rose, D. W., Hooshmand, F., Aggarwal, A. K., & Rosenfeld, M. G. (2000) · Science · doi:10.1126/science.290.5494.1127 · Cited by 244

Regulation of the Th2 Cytokine Locus by a Locus Control Region

Lee, G. R., Fields, P. E., Griffin, T. J., & Flavell, R. A. (2003) · Immunity · doi:10.1016/s1074-7613(03)00179-1 · Cited by 234

Gamma delta beta-thalassemia due to a de novo mutation deleting the 5' beta-globin gene activation-region hypersensitive sites.

Driscoll, M. C., Dobkin, C. S., & Alter, B. P. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.19.7470 · Cited by 233

Platelet characteristics in patients with X-linked macrothrombocytopenia because of a novel GATA1mutation

Freson, K., Devriendt, K., Matthijs, G., Hoof, A. V., Vos, R. D., Thys, C., Minner, K., Hoylaerts, M., Vermylen, J., & Geet, C. V. (2001) · Blood · doi:10.1182/blood.v98.1.85 · Cited by 232

Intergenic transcription through a Polycomb group response element counteracts silencingPreprint

Schmitt, S., Prestel, M., & Paro, R. (2005) · Genes & Development · doi:10.1101/gad.326205 · Cited by 230

The MTE, a new core promoter element for transcription by RNA polymerase IIPreprint

Lim, C. Y., Santoso, B., Boulay, T., Dong, E., Ohler, U., & Kadonaga, J. T. (2004) · Genes & Development · doi:10.1101/gad.1193404 · Cited by 230

Loss-of-Function Mutations in the LIM-Homeodomain Gene, LMX1B, in Nail-Patella Syndrome

Vollrath, D., Jaramillo-Babb, V. L., Clough, M. V., McIntosh, I., Scott, K. M., Lichter, P. R., & Richards, J. E. (1998) · Human Molecular Genetics · doi:10.1093/hmg/7.7.1091 · Cited by 216

Regulation of human fetal hemoglobin: new players, new complexities

Bank, A. (2005) · Blood · doi:10.1182/blood-2005-05-2113 · Cited by 213

DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs

Suzuki, Y. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.328 · Cited by 213

Origins of leukaemia in children with Down syndrome

Hitzler, J. K., & Zipursky, A. (2005) · Nature reviews. Cancer · doi:10.1038/nrc1525 · Cited by 209

Evaluation of regulatory potential and conservation scores for detecting cis -regulatory modules in aligned mammalian genome sequencesPreprint

King, D. C., Taylor, J., Elnitski, L., Chiaromonte, F., Miller, W., & Hardison, R. C. (2005) · Genome Research · doi:10.1101/gr.3642605 · Cited by 208

X-linked thrombocytopenia caused by a novel mutation ofGATA-1

Mehaffey, M. G., Newton, A., Gandhi, M. J., Crossley, M., & Drachman, J. G. (2001) · Blood · doi:10.1182/blood.v98.9.2681 · Cited by 199

beta-Thalassemia in American Blacks: novel mutations in the "TATA" box and an acceptor splice site.

Antonarakis, S. E., Irkin, S. H., Cheng, T. C., Scott, A. F., Sexton, J. P., Trusko, S. P., Charache, S., & Kazazian, H. H. (1984) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.81.4.1154 · Cited by 191

DNA methylation and cancer therapy: new developments and expectations

Esteller, M. (2004) · Current Opinion in Oncology · doi:10.1097/01.cco.0000147383.04709.10 · Cited by 184

Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites

Crawford, G. E., Holt, I. E., Mullikin, J. C., Tai, D. S., Green, E. D., Wolfsberg, T. G., & Collins, F. S. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307540100 · Cited by 184

Effects of altered gene order or orientation of the locus control region on human β-globin gene expression in mice

Tanimoto, K., Liu, Q., Bungert, J., & Engel, J. D. (1999) · Nature · doi:10.1038/18698 · Cited by 178

Frequent somatic mutations of the transcription factor ATBF1 in human prostate cancer

Sun, X., Frierson, H. F., Chen, C., Li, C., Ran, Q., Otto, K. B., Cantarel, B. L., Vessella, R. L., Gao, A. C., Petros, J. A., et al. (2005) · Nature Genetics · doi:10.1038/ng1528 · Cited by 174

FootPrinter: a program designed for phylogenetic footprinting

Blanchette, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg606 · Cited by 172

Expanding functional diversity of the coactivators

Lonard, D. M., & O'Malley, B. W. (2005) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2005.01.001 · Cited by 172

Synergy of human Pol II core promoter elements revealed by statistical sequence analysis

Gershenzon, N., & Ioshikhes, I. P. (2005) · Bioinform. · doi:10.1093/bioinformatics/bti172 · Cited by 168

CREB Binds to Multiple Loci on Human Chromosome 22

Euskirchen, G. M., Royce, T. E., Bertone, P., Martone, R., Rinn, J. L., Nelson, F. K., Sayward, F., Luscombe, N. M., Miller, P. L., Gerstein, M., et al. (2004) · Molecular and Cellular Biology · doi:10.1128/mcb.24.9.3804-3814.2004 · Cited by 166

COMPARATIVE GENOMICS

Miller, W., Makova, K. D., Nekrutenko, A., & Hardison, R. C. (2004) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.5.061903.180057 · Cited by 165

Defect of histone acetyltransferase activity of the nuclear transcriptional coactivator CBP in Rubinstein-Taybi syndrome

Murata, T. (2001) · Human Molecular Genetics · doi:10.1093/hmg/10.10.1071 · Cited by 164

Identification of a hot spot for microdeletions in patients with X- linked deafness type 3 (DFN3) 900 kb proximal to the DFN3 gene POU3F4

de Kok, Y. (1996) · Human Molecular Genetics · doi:10.1093/hmg/5.9.1229 · Cited by 164

Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis

Mooney, S. D. (2005) · Briefings in Bioinformatics · doi:10.1093/bib/6.1.44 · Cited by 163

Promoter prediction analysis on the whole human genome

Bajić, V. B., Tan, S. L., Suzuki, Y., & Sugano, S. (2004) · Nature Biotechnology · doi:10.1038/nbt1032 · Cited by 157

Large-scale enhancer detection in the zebrafish genome

Ellingsen, S., Laplante, M. A., König, M., Kikuta, H., Furmanek, T., Høivik, E. A., & Becker, T. S. (2005) · Development · doi:10.1242/dev.01951 · Cited by 157

Chromatin Insulators and Boundaries: Effects on Transcription and Nuclear Organization

Gerasimova, T. I., & Corces, V. G. (2001) · Annual Review of Genetics · doi:10.1146/annurev.genet.35.102401.090349 · Cited by 157

Enhancers: Mechanisms of Action and Cell Specificity

Atchison, M. L. (1988) · Annual Review of Cell Biology · doi:10.1146/annurev.cb.04.110188.001015 · Cited by 157

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

Identification of a Mutation in a GATA Binding Site of the Platelet Glycoprotein Ibβ Promoter Resulting in the Bernard-Soulier Syndrome

Ludlow, L. B., Schick, B. P., Budarf, M. L., Driscoll, D. A., Zackai, E. H., Cohen, A. R., & Konkle, B. A. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.36.22076 · Cited by 147

Disruption of a C/EBP binding site in the factor IX promoter is associated with haemophilia B

Crossley, M., & Brownlee, G. G. (1990) · Nature · doi:10.1038/345444a0 · Cited by 145

DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise

Vilar, J. M. G., & Saiz, L. (2005) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2005.02.005 · Cited by 142

Microdeletion of target sites for insulator protein CTCF in a chromosome 11p15 imprinting center in Beckwith–Wiedemann syndrome and Wilms' tumor

Prawitt, D., Enklaar, T., Gärtner-Rupprecht, B., Spangenberg, C., Oswald, M., Lausch, E. U., Schmidtke, P., Reutzel, D., Fees, S. A., Lucito, R., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0500037102 · Cited by 130

The role of enhancers as centres for general transcription factor recruitment

Szutorisz, H., Dillon, N., & Tora, L. (2005) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2005.08.006 · Cited by 125

Functional Characterization of Core Promoter Elements: the Downstream Core Element Is Recognized by TAF1

Lee, D., Gershenzon, N. I., Gupta, M., Ioshikhes, I. P., Reinberg, D., & Lewis, B. A. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.21.9674-9686.2005 · Cited by 122

SWI/SNF Chromatin-Remodeling Factors Induce Changes in DNA Methylation to Promote Transcriptional Activation

Banine, F., Bartlett, C. S., Gunawardena, R. W., Muchardt, C., Yaniv, M., Knudsen, E. S., Weissman, B. E., & Sherman, L. S. (2005) · Cancer Research · doi:10.1158/0008-5472.can-04-3554 · Cited by 118

Large-scale structural analysis of the core promoter in mammalian and plant genomes

Florquin, K. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki737 · Cited by 117

Boundary elements and nuclear organization

Capelson, M., & Corces, V. G. (2004) · Biology of the Cell · doi:10.1016/j.biolcel.2004.06.004 · Cited by 116

YY1 DNA binding and PcG recruitment requires CtBPPreprint

Srinivasan, L., & Atchison, M. L. (2004) · Genes & Development · doi:10.1101/gad.1228204 · Cited by 116

Mechanism of Transcriptional Silencing in Yeast

Chen, L., & Widom, J. (2005) · Cell · doi:10.1016/j.cell.2004.11.030 · Cited by 112

Alpha-thalassemia caused by a large (62 kb) deletion upstream of the human alpha globin gene cluster

Hatton, C., Wilkie, A. O. M., Drysdale, H. C., Wood, W., Vickers, M. A., Sharpe, J. A., Ayyub, H., Pretorius, I., Buckle, V., & Higgs, D. R. (1990) · Blood · doi:10.1182/blood.v76.1.221.221 · Cited by 109

DNA recognition by nuclear receptors

Claessens, F., & Gewirth, D. T. (2004) · Essays in Biochemistry · doi:10.1042/bse0400059 · Cited by 108

A mutation in the promoter of the lipoprotein lipase (LPL) gene in a patient with familial combined hyperlipidemia and low LPL activity.

Yang, W. S., Nevin, D. N., Peng, R., Brunzell, J. D., & Deeb, S. S. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.10.4462 · Cited by 108

Functional Analysis of the Human Adenosine Deaminase Gene Thymic Regulatory Region and Its Ability To Generate Position-Independent Transgene Expression

Aronow, B. J., Silbiger, R. N., Dusing, M. R., Stock, J. L., Yager, K. L., Potter, S. S., Hutton, J. J., & Wiginton, D. A. (1992) · Molecular and Cellular Biology · doi:10.1128/mcb.12.9.4170 · Cited by 105

The role of DNA response elements as allosteric modulators of steroid receptor function

Geserick, C., Meyer, H., & Haendler, B. (2005) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2005.03.007 · Cited by 102

A single-base substitution in the proximal Sp1 site of the human low density lipoprotein receptor promoter as a cause of heterozygous familial hypercholesterolemia.

Koivisto, U., Palvimo, J. J., Jänne, O. A., & Kontula, K. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.22.10526 · Cited by 101

The multicoloured world of promoter recognition complexes

Müller, F., & Tora, L. (2003) · The EMBO Journal · doi:10.1038/sj.emboj.7600027 · Cited by 98

Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity

Yamashita, R., Suzuki, Y., Sugano, S., & Nakai, K. (2005) · Gene · doi:10.1016/j.gene.2005.01.012 · Cited by 93

Uroporphyrinogen III synthase erythroid promoter mutations in adjacent GATA1 and CP2 elements cause congenital erythropoietic porphyria

Solis, C., Aizencang, G. I., Astrin, K. H., Bishop, D. F., & Desnick, R. J. (2001) · Journal of Clinical Investigation · doi:10.1172/jci10642 · Cited by 93

Eukaryotic Transcription Activation: Right on Target

Green, M. R. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.04.017 · Cited by 92

Chromatin Boundaries and Chromatin DomainsPreprint

Felsenfeld, G., Burgess-Beusse, B. L., Farrell, C. M., Gaszner, M., Ghirlando, R., Huang, S.-L., Jin, C., Litt, M. D., Magdinier, F., Mutskov, V. J., et al. (2004) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2004.69.245 · Cited by 92

The Human Enhancer Blocker CTC-binding Factor Interacts with the Transcription Factor Kaiso

Defossez, P., Kelly, K. F., Filion, G. J. P., Pérez‐Torrado, R., Magdinier, F., Menoni, H., Nordgaard, C. L., Daniel, J. M., & Gilson, É. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m510802200 · Cited by 88

Synergistic repression of anaerobic genes by Mot3 and Rox1 in Saccharomyces cerevisiae

Sertil, O. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg792 · Cited by 88

A downstream element in the human β-globin promoter: Evidence of extended sequence-specific transcription factor IID contacts

Lewis, B. A., Kim, T.-K., & Orkin, S. H. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.120181197 · Cited by 87

Direct isolation and identification of promoters in the human genomePreprint

Kim, T. H., Barrera, L. O., Qu, C., Calcar, S. V., Trinklein, N. D., Cooper, S. J., Luna, R. M., Glass, C. K., Rosenfeld, M. G., Myers, R., et al. (2005) · Genome Research · doi:10.1101/gr.3430605 · Cited by 86

Prospects and implications of using chromatin insulators in gene therapy and transgenesis.

Recillas-Targa, F., Valadez-Graham, V., & Farrell, C. (2004) · Bioessays · doi:10.1002/bies.20059 · Cited by 85

Chromosome‐mediated alterations of the MYC gene in human cancer

Popescu, N. C., & Zimonjic, D. B. (2002) · Journal of Cellular and Molecular Medicine · doi:10.1111/j.1582-4934.2002.tb00183.x · Cited by 83

Direct regulation ofknotgene expression by Ultrabithorax and the evolution of cis-regulatory elements inDrosophila

Hersh, B. M., & Carroll, S. B. (2005) · Development · doi:10.1242/dev.01737 · Cited by 83

Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo

Papatsenko, D., & Levine, M. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409414102 · Cited by 82

Strong bias in the location of functional promoter polymorphisms

Buckland, P. R., Hoogendoorn, B., Coleman, S. L., Guy, C., Smith, S. K., & O’Donovan, M. C. (2005) · Human Mutation · doi:10.1002/humu.20207 · Cited by 81

cis -Regulatory Logic of Short-Range Transcriptional Repression in Drosophila melanogaster

Kulkarni, M. M., & Arnosti, D. N. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.9.3411-3420.2005 · Cited by 75

Towards therapeutic applications of engineered zinc finger proteins

Klug, A. (2004) · FEBS Letters · doi:10.1016/j.febslet.2004.10.104 · Cited by 74

Delta-thalassemia caused by disruption of the site for an erythroid- specific transcription factor, GATA-1, in the delta-globin gene promoter

Matsuda, M., Sakamoto, N., & Fukumaki, Y. (1992) · Blood · doi:10.1182/blood.v80.5.1347.1347 · Cited by 72

Nongenic transcription, gene regulation and action at a distance

Cook, P. R. (2003) · Journal of Cell Science · doi:10.1242/jcs.00819 · Cited by 72

From an Enhanceosome to a Repressosome: Molecular Antagonism between Glucocorticoids and EGF Leads to Inhibition of Wound Healing

Lee, B., Vouthounis, C., Stojadinović, O., Brem, H., Im, M. J., & Tomic‐Canic, M. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.11.027 · Cited by 71

Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites

Balhoff, J. P., & Wray, G. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409638102 · Cited by 69

Insulator dynamics and the setting of chromatin domains

Fourel, G., Magdinier, F., & Gilson, É. (2004) · BioEssays · doi:10.1002/bies.20028 · Cited by 65

Thalassemia intermedia: moderate reduction of beta globin gene transcriptional activity by a novel mutation of the proximal CACCC promoter element

Kulozik, A. E., Bellan-Koch, A., Bail, S., KOHNE, E., & Kleihauer, E. (1991) · Blood · doi:10.1182/blood.v77.9.2054.bloodjournal7792054 · Cited by 64

Gene Annotation: Prediction and Testing

Ashurst, J. L., & Collins, J. E. (2003) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.4.070802.110300 · Cited by 64

Redundancy of information in enhancers as a principle of mammalian transcription control

Schaffner, G., Schirm, S., Müller-Baden, B., Weber, F., & Schaffner, W. (1988) · Journal of Molecular Biology · doi:10.1016/0022-2836(88)90440-8 · Cited by 62

Activator effect of coinjected enhancers on the muscle-specific expression of promoters in zebrafish embryos

Müller, F., Williams, D. W., Kobolák, J., Gauvry, L., Goldspink, G., Orbán, L., & Maclean, N. (1997) · Molecular Reproduction and Development · doi:10.1002/(sici)1098-2795(199708)47:4 · Cited by 61

Prediction of cis-regulatory elements using binding site matrices — the successes, the failures and the reasons for both

Vavouri, T., & Elgar, G. (2005) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2005.05.002 · Cited by 61

Altered Spacing of Promoter Elements Due to the Dodecamer Repeat Expansion Contributes to Reduced Expression of the Cystatin B Gene in EPM1

Lalioti, M. D., Scott, H. S., & Antonarakis, S. E. (1999) · Human Molecular Genetics · doi:10.1093/hmg/8.9.1791 · Cited by 55

Repression of an Interleukin-4-responsive Promoter Requires Cooperative BCL-6 Function

Harris, M. B., Mostecki, J. W., & Rothman, P. B. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m412649200 · Cited by 54

A new PKLR gene mutation in the R‐type promoter region affects the gene transcription causing pyruvate kinase deficiency

Manco, L., Ribeiro, L., Máximo, V., Almeida, H., Costa, A. S. A., Freitas, O., Barbot, J., Abade, A., & Tamagnini, G. P. (2000) · British Journal of Haematology · doi:10.1046/j.1365-2141.2000.02283.x · Cited by 53

GATA Transcription Factors in Hematologic Disease

Cantor, A. B. (2005) · International Journal of Hematology · doi:10.1532/ijh97.04180 · Cited by 51

The mammalian Mediator complex

Conaway, J. W., Florens, L. A., Sato, S., Tomomori‐Sato, C., Parmely, T. J., Yao, T., Swanson, S. K., Banks, C. A. S., Washburn, M. P., & Conaway, R. C. (2004) · FEBS Letters · doi:10.1016/j.febslet.2004.11.031 · Cited by 49

em E2 em A basic helix-loop-helix transcription factors in human leukemia

LeBrun, D. P. (2003) · Frontiers in bioscience · doi:10.2741/1030 · Cited by 48

Hierarchical Interactions Control CD4 Gene Expression during Thymocyte Development

Adlam, M., & Siu, G. (2003) · Immunity · doi:10.1016/s1074-7613(03)00021-9 · Cited by 47

A statistical analysis of the TRANSFAC database

Fogel, G. B., Weekes, D., Varga, G., Dow, E. R., Craven, A. M., Harlow, H. B., Su, E. W., Onyia, J. E., & Chen, S. (2005) · Biosystems · doi:10.1016/j.biosystems.2005.03.003 · Cited by 47

TRADE-OFFS IN DETECTING EVOLUTIONARILY CONSTRAINED SEQUENCE BY COMPARATIVE GENOMICS

Stone, E. A., Cooper, G. M., & Sidow, A. (2005) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.6.080604.162146 · Cited by 45

A novel silent β‐thalassemia mutation in the distal CACCC box affects the binding and responsiveness to EKLF

Moi, P., Faà, V., Marini, M. G., Asunis, I., Ibba, G., Cao, A., & Rosatelli, M. C. (2004) · British Journal of Haematology · doi:10.1111/j.1365-2141.2004.05146.x · Cited by 41

An evolutionary constraint: Strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules

Cameron, R. A., Chow, S. H., Berney, K., Chiu, T.-Y., Yuan, Q. A., Krämer, A., Helguero, A., Ransick, A., Yun, M., & Davidson, E. H. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0505291102 · Cited by 41

Deletion analysis of the human CD2 gene locus control region in transgenic mice

Lang, G., Mamalaki, C., Greenberg, D., Yannoutsos, N., & Kioussis, D. (1991) · Nucleic Acids Research · doi:10.1093/nar/19.21.5851 · Cited by 40

Long-range comparison of human and mouse Sprr loci to identify conserved noncoding sequences involved in coordinate regulationPreprint

Martín, N., Patel, S., & Segre, J. A. (2004) · Genome Research · doi:10.1101/gr.2709404 · Cited by 38

Enhancer Choice in Cis and in Trans in Drosophila melanogaster

Morris, J. R., Petrov, D. A., Lee, A. M., & Wu, C.-T. (2004) · Genetics · doi:10.1534/genetics.104.026955 · Cited by 38

Recruitment of a Repressosome Complex at the Growth Hormone Receptor Promoter and Its Potential Role in Diabetic Nephropathy

Gowri, P. M., Yu, J. H., Shaufl, A. L., Sperling, M. A., & Menon, R. K. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.3.815-825.2003 · Cited by 38

A functional SNP in the promoter region of TCOF1 is associated with reduced gene expression and YY1 DNA–protein interaction

Masotti, C., Armelin‐Correa, L., Splendore, A., Lin, C. J., Barbosa, A. S., Sogayar, M. C., & Passos‐Bueno, M. R. (2005) · Gene · doi:10.1016/j.gene.2005.06.004 · Cited by 37

Core Promoter Elements and TAFs Contribute to the Diversity of Transcriptional Activation in Vertebrates

Chen, Z., & Manley, J. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.20.7350-7362.2003 · Cited by 36

ATG deserts define a novel core promoter subclassPreprint

Lee, M. P., Howcroft, T. K., Kotekar, A., Yang, H. H., Buetow, K. H., & Singer, D. S. (2005) · Genome Research · doi:10.1101/gr.3873705 · Cited by 30

Structural Analysis and Mapping of DNase I Hypersensitivity of HS5 of the β-Globin Locus Control Region

Li, Q., Zhang, M., Duan, Z., & Stamatoyannopoulos, G. (1999) · Genomics · doi:10.1006/geno.1999.5954 · Cited by 29

Evolution of regulatory elements producing a conserved gene expression pattern in Caenorhabditis

Wang, X., Greenberg, J. F., & Chamberlin, H. (2004) · Evolution & Development · doi:10.1111/j.1525-142x.2004.04029.x · Cited by 27

Development of pro-angiogenic engineered transcription factors for the treatment of cardiovascular disease

Rebar, E. J. (2004) · Expert Opinion on Investigational Drugs · doi:10.1517/13543784.13.7.829 · Cited by 27

Oncogenic protein tyrosine kinases

Saglio, G. N., & Cilloni, D. (2004) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-004-4271-0 · Cited by 26

Developmental Regulation of the β-Globin Gene Locus

Chakalova, L., Carter, D., Debrand, E., Goyenechea, B., Horton, A., Miles, J., Osborne, C. S., & Fraser, P. (2005) · Springer eBooks · doi:10.1007/3-540-27310-7_8 · Cited by 25

Point mutation associated with X-linked dominant Charcot-Marie-Tooth disease impairs the P2 promoter activity of human connexin-32 gene

Wang, H.-L., Wu, T., Chang, W.-T., Li, A. H., Chen, M.-S., Wu, C., & Fang, W. (2000) · Molecular Brain Research · doi:10.1016/s0169-328x(00)00087-5 · Cited by 24

Differential transcription factor occupancy but evolutionarily conserved chromatin features at the human and mouse M-CSF (CSF-1) receptor loci

Follows, G. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg804 · Cited by 18

Igf2/H19 Imprinting Control Region (ICR): An Insulator or a Position-Dependent Silencer?

Banerjee, S., Smallwood, A., Lamond, S., Campbell, S. C., & Nargund, G. (2001) · The Scientific World JOURNAL · doi:10.1100/tsw.2001.50 · Cited by 13

The mouse genome: Experimental examination of gene predictions and transcriptional start sitesPreprint

Dike, S., Balija, V. S., Nascimento, L. U., Xuan, Z., Ou, J., Zutavern, T., Palmer, L. E., Hannon, G. J., Zhang, M. Q., & McCombie, W. R. (2004) · Genome Research · doi:10.1101/gr.3158304 · Cited by 12

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

GREAT improves functional interpretation of cis-regulatory regions

McLean, C. Y., Bristor, D., Hiller, M., Clarke, S. L., Schaar, B. T., Lowe, C. B., Wenger, A. M., & Bejerano, G. (2010) · Nature Biotechnology · doi:10.1038/nbt.1630 · Cited by 4,502

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.035 · Cited by 4,143

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716

Super-enhancers in the control of cell identity and disease

Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., Hoke, H. A., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.09.053 · Cited by 3,662

Mapping genomic loci implicates genes and synaptic biology in schizophrenia

Trubetskoy, V., Pardiñas, A. F., Qi, T., Panagiotaropoulou, G., Awasthi, S., Bigdeli, T. B., Bryois, J., Chen, C.-Y., Dennison, C. A., Hall, L. S., et al. (2022) · Nature · doi:10.1038/s41586-022-04434-5 · Cited by 2,964

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

Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction

Bkhetan, Z. A., & Plewczyński, D. (2018) · Scientific Reports · doi:10.1038/s41598-018-23276-8 · Cited by 1,672

Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection

GERAD1 Consortium, Pardiñas, A. F., CRESTAR Consortium, Holmans, P., Pocklington, A. J., Escott-Price, V., Ripke, S., Carrera, N., Legge, S. E., Bishop, S., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0059-2 · Cited by 1,552

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 User's Guide to the Encyclopedia of DNA Elements (ENCODE)

The ENCODE Project Consortium (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001046 · Cited by 1,515

Enhancer function: new insights into the regulation of tissue-specific gene expression

Ong, C.-T., & Corces, V. G. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2957 · Cited by 929

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factorsPreprint

Wang, J., Zhuang, J., Iyer, S., Lin, X.-Y., Whitfield, T. W., Greven, M. C., Pierce, B. G., Dong, X., Kundaje, A. B., Cheng, Y., et al. (2012) · Genome Research · doi:10.1101/gr.139105.112 · Cited by 827

Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways

The Network and Pathway Analysis Subgroup of the Psychiatric Genomics Consortium (2015) · Nature Neuroscience · doi:10.1038/nn.3922 · Cited by 755

Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics

Wang, Y., Zhang, S., Li, F., Zhou, Y., Zhang, Y., Wang, Z., Zhang, R., Zhu, J., Ren, Y., Tan, Y. C., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz981 · Cited by 798

Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus

Xiang, J., Yin, Q.-F., Chen, T., Zhang, Y., Zhang, X.-O., Wu, Z., Zhang, S., Wang, H., Ge, J., Lu, X., et al. (2014) · Cell Research · doi:10.1038/cr.2014.35 · Cited by 741

Genomic views of distant-acting enhancers

Visel, A., Rubin, E. M., & Pennacchio, L. A. (2009) · Nature · doi:10.1038/nature08451 · Cited by 610

Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements

Barrett, L. W., Fletcher, S., & Wilton, S. D. (2012) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-012-0990-9 · Cited by 641

High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation

Veyrieras, J.-B., Kudaravalli, S., Kim, S. Y., Dermitzakis, E. T., Gilad, Y., Stephens, M., & Pritchard, J. K. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000214 · Cited by 536

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 562

eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

Mousavi, K., Zare, H., Dell’Orso, S., Grøntved, L., Gutierrez-Cruz, G., Derfoul, A., Hager, G. L., & Sartorelli, V. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.07.022 · Cited by 528

The Ensembl Regulatory Build

Zerbino, D. R., Wilder, S. P., Johnson, N., Juettemann, T., & Flicek, P. R. (2015) · Genome Biology · doi:10.1186/s13059-015-0621-5 · Cited by 429

From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis

Yan, F., Powell, D., Curtis, D. J., & Wong, N. C. (2020) · Genome biology · doi:10.1186/s13059-020-1929-3 · Cited by 487

The RNA Polymerase II Carboxy-Terminal Domain (CTD) Code

Eick, D., & Geyer, M. (2013) · Chemical Reviews · doi:10.1021/cr400071f · Cited by 500

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

Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin

Whalen, S., Truty, R. M., & Pollard, K. S. (2016) · Nature Genetics · doi:10.1038/ng.3539 · Cited by 456

Editing the epigenome: technologies for programmable transcription and epigenetic modulation

Thakore, P. I., Black, J. B., Hilton, I. B., & Gersbach, C. A. (2016) · Nature Methods · doi:10.1038/nmeth.3733 · Cited by 451

ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data

Zhou, K., Liu, S., Sun, W., Zheng, L., Zhou, H., Yang, J., & Qu, L. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw965 · Cited by 417

H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions

Cai, Y., Zhang, Y., Loh, Y. P., Tng, J. Q., Lim, M. C., Cao, Z., Raju, A., Lieberman Aiden, E., Li, S., Manikandan, L., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-20940-y · Cited by 321

Identification of genetic variants associated with Huntington's disease progression: a genome-wide association study

Moss, D. J. H., Pardiñas, A. F., Langbehn, D., Lo, K., Leavitt, B. R., Roos, R., Durr, A., Mead, S., Coleman, A., Santos, R. D., et al. (2017) · The Lancet Neurology · doi:10.1016/s1474-4422(17)30161-8 · Cited by 312

Enhancers as information integration hubs in development: lessons from genomics

Buecker, C., & Wysocka, J. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.02.008 · Cited by 295

A cellular and molecular view of T helper 17 cell plasticity in autoimmunity

Stadhouders, R., Lubberts, E., & Hendriks, R. W. (2017) · Journal of Autoimmunity · doi:10.1016/j.jaut.2017.12.007 · Cited by 300

Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets

Leung, M. K. K., Delong, A., Alipanahi, B., & Frey, B. J. (2015) · Proceedings of the IEEE · doi:10.1109/jproc.2015.2494198 · Cited by 284

Promoter DNA Hypermethylation and Paradoxical Gene Activation

Smith, J., Sen, S., Weeks, R. J., Eccles, M. R., & Chatterjee, A. (2020) · Trends in cancer · doi:10.1016/j.trecan.2020.02.007 · Cited by 268

ChIP‐based methods for the identification of long‐range chromatin interactions

Fullwood, M. J., & Ruan, Y. (2009) · Journal of Cellular Biochemistry · doi:10.1002/jcb.22116 · Cited by 251

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

Yip, K. Y.-L., Cheng, C., Bhardwaj, N., Brown, J., Leng, J., Kundaje, A. B., Rozowsky, J. S., Birney, E., Bickel, P. J., Snyder, M. P., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-9-r48 · Cited by 248

Genomic approaches towards finding cis-regulatory modules in animals

Hardison, R. C., & Taylor, J. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3242 · Cited by 245

Finding distal regulatory elements in the human genome

Heintzman, N. D., & Ren, B. (2009) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2009.09.006 · Cited by 241

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

Cheng, Y., Wu, W., Ashok Kumar, S., Yu, D., Deng, W., Tripic, T., King, D. C., Chen, K.-B., Zhang, Y., Drautz, D., et al. (2009) · Genome Research · doi:10.1101/gr.098921.109 · Cited by 223

Progesterone receptors, their isoforms and progesterone regulated transcription

Jacobsen, B. M., & Horwitz, K. B. (2011) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2011.09.016 · Cited by 229

An Overview of Genome Organization and How We Got There: from FISH to Hi-C

Fraser, J., Williamson, I., Bickmore, W. A., & Dostie, J. (2015) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00006-15 · Cited by 232

Predictive chromatin signatures in the mammalian genome

Hon, G. C., Hawkins, R. D., & Ren, B. (2009) · Human Molecular Genetics · doi:10.1093/hmg/ddp409 · Cited by 231

DBTSS: database of transcription start sites, progress report 2008

Wakaguri, H., Yamashita, R., Suzuki, Y., Sugano, S., & Nakai, K. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm901 · Cited by 221

Enhancers: The abundance and function of regulatory sequences beyond promoters

Bulger, M., & Groudine, M. T. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2009.11.035 · Cited by 192

Transcription factors mediate long-range enhancer–promoter interactions

Nolis, I. K., McKay, D. J., Mantouvalou, E., Lomvardas, S., Merika, M., & Thanos, D. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0902454106 · Cited by 197

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 186

Identification and dynamic quantification of regulatory elements using total RNAPreprint

Duttke, S. H. C., Chang, M. W., Heinz, S., & Benner, C. W. (2019) · Genome Research · doi:10.1101/gr.253492.119 · Cited by 175

Systematic identification of silencers in human cells

Pang, B., & Snyder, M. P. (2020) · Nature Genetics · doi:10.1038/s41588-020-0578-5 · Cited by 183

Discovery and Annotation of Functional Chromatin Signatures in the Human Genome

Hon, G. C., Wang, W., & Ren, B. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000566 · Cited by 181

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 176

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 170

Transcriptional response to stress is pre-wired by promoter and enhancer architecture

Vihervaara, A., Mahat, D. B., Guertin, M. J., Chu, T., Danko, C. G., Lis, J. T., & Sistonen, L. (2017) · Nature Communications · doi:10.1038/s41467-017-00151-0 · Cited by 164

Silencing by imprinted noncoding RNAs: is transcription the answer?

Pauler, F. M., Koerner, M. V., & Barlow, D. P. (2007) · Trends in Genetics · doi:10.1016/j.tig.2007.03.018 · Cited by 156

Genome organization and long-range regulation of gene expression by enhancers

Smallwood, A., & Ren, B. (2013) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2013.02.005 · Cited by 155

Ensembl Genome Browser

Fernández, X. M., & Birney, E. (2009) · Springer eBooks · doi:10.1007/978-3-540-37654-5_45 · Cited by 156

Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mappingPreprint

Walhout, A. J. M. (2006) · Genome Research · doi:10.1101/gr.5321506 · Cited by 161

iEnhancer-5Step: Identifying enhancers using hidden information of DNA sequences via Chou's 5-step rule and word embedding

Le, N. Q. K., Yapp, E. K. Y., Ho, Q., Nagasundaram, N., Ou, Y., & Yeh, H. (2019) · Analytical Biochemistry · doi:10.1016/j.ab.2019.02.017 · Cited by 152

The Hierarchy of Transcriptional Activation: From Enhancer to Promoter

Vernimmen, D., & Bickmore, W. A. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.10.004 · Cited by 155

Characterization of human epigenomes

Wang, Z., Schones, D. E., & Zhao, K. (2009) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2009.02.001 · Cited by 160

Enhancers: emerging roles in cell fate specification

Ong, C., & Corces, V. G. (2012) · The EMBO Reports · doi:10.1038/embor.2012.52 · Cited by 144

Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes

Wang, Q. S., Pierce‐Hoffman, E., Cummings, B. B., Alföldi, J., Francioli, L. C., Gauthier, L. D., Hill, A. J., O’Donnell‐Luria, A., Genome Aggregation Database Production Team, Armean, I. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-12438-5 · Cited by 149

Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development

Ngan, C. Y., Wong, C. H., Tjong, H., Wang, W., Goldfeder, R. L., Choi, C., He, H., Gong, L., Lin, J., Urban, B., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0581-x · Cited by 140

Activation of P-TEFb by Androgen Receptor-Regulated Enhancer RNAs in Castration-Resistant Prostate Cancer

Zhao, Y., Wang, L., Ren, S., Wang, L., Blackburn, P. R., McNulty, M. S., Gao, X., Qiao, M., Vessella, R. L., Kohli, M., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.03.038 · Cited by 137

Analysis of Dll4 regulation reveals a combinatorial role for Sox and Notch in arterial development

Sacilotto, N., Monteiro, R. M., Fritzsche, M., Becker, P., Sánchez‐del‐Campo, L., Liu, K., Pinheiro, P., Ratnayaka, I., Davies, B., Goding, C. R., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1300805110 · Cited by 134

A predictive modeling approach for cell line-specific long-range regulatory interactions

Roy, S., Siahpirani, A. F., Chasman, D. A., Knaack, S., Ay, F., Stewart, R. M., Wilson, M. D., & Sridharan, R. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv865 · Cited by 123

DEEP: a general computational framework for predicting enhancers

Kleftogiannis, D., Kalnis, P., & Bajic, V. B. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1058 · Cited by 125

Nuclear Organization and Genome Function

Bortle, K. V., & Corces, V. G. (2012) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-101011-155824 · Cited by 127

In silico prediction of high-resolution Hi-C interaction matrices

Zhang, S., Chasman, D. A., Knaack, S., & Roy, S. (2019) · Nature Communications · doi:10.1038/s41467-019-13423-8 · Cited by 119

A Brief Review on the Human Encyclopedia of DNA Elements (ENCODE) Project

Qu, H., & Fang, X. (2013) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2013.05.001 · Cited by 124

Chromatin-Driven Behavior of Topologically Associating Domains

Ciabrelli, F., & Cavalli, G. (2014) · Journal of Molecular Biology · doi:10.1016/j.jmb.2014.09.013 · Cited by 123

In the loop: promoter–enhancer interactions and bioinformatics

Mora, A., Sandve, G. K., Gabrielsen, O. S., & Eskeland, R. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv097 · Cited by 126

What does our genome encode?Preprint

Stamatoyannopoulos, J. A. (2012) · Genome Research · doi:10.1101/gr.146506.112 · Cited by 120

Genome-wide discovery of human heart enhancersPreprint

Narlikar, L., Sakabe, N. J., Blanski, A. A., Arimura, F. E., Westlund, J. M., Nóbrega, M. A., & Ovcharenko, I. (2010) · Genome Research · doi:10.1101/gr.098657.109 · Cited by 121

Promoter analysis and prediction in the human genome using sequence-based deep learning models

Umarov, R. K., Kuwahara, H., Li, Y., Gao, X., & Solovyev, V. V. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty1068 · Cited by 120

Cis-regulatory mutations in human disease

Epstein, D. J. (2009) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/elp021 · Cited by 117

Identifying regulatory elements in eukaryotic genomes

Narlikar, L., & Ovcharenko, I. (2009) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/elp014 · Cited by 122

Regulatory variants: from detection to predicting impact

Rojano, E., Seoane, P., Ranea, J. A. G., & Perkins, J. R. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bby039 · Cited by 120

Chromatin and epigenetic features of long-range gene regulation

Harmston, N., & Lenhard, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt499 · Cited by 111

Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene

Gheldof, N., Smith, E. M., Tabuchi, T. M., Koch, C. M., Dunham, I., Stamatoyannopoulos, J. A., & Dekker, J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq175 · Cited by 114

Predicting enhancers with deep convolutional neural networks

Xu, M., Zeng, W., Chen, S., Chen, N., Chen, T., & Jiang, R. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1878-3 · Cited by 107

New approaches for genome assembly and scaffolding

Rice, E. S., & Green, R. E. (2019) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-020518-115344 · Cited by 110

Helper T‐cell identity and evolution of differential transcriptomes and epigenomes

Vahedi, G., Poholek, A. C., Hand, T. W., Laurence, A. D. J., Kanno, Y., O’Shea, J. J., & Hirahara, K. (2013) · Immunological Reviews · doi:10.1111/imr.12037 · Cited by 112

Pharmacogenomics in Alzheimer's Disease

Cacabelos, R. (2008) · Methods in molecular biology · doi:10.1007/978-1-59745-205-2_10 · Cited by 109

MPRAnalyze: statistical framework for massively parallel reporter assays

Ashuach, T., Fischer, D. S., Kreimer, A., Ahituv, N., Theis, F. J., & Yosef, N. (2019) · Genome biology · doi:10.1186/s13059-019-1787-z · Cited by 105

Integrative genomic analysis reveals widespread enhancer regulation by p53 in response to DNA damage

Younger, S. T., Kenzelmann-Broz, D., Jung, H., Attardi, L. D., & Rinn, J. L. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv284 · Cited by 99

Engineering Promoter Architecture in Oleaginous Yeast Yarrowia lipolytica

Hussain, M. S., Gambill, L., Smith, S., & Blenner, M. (2015) · ACS Synthetic Biology · doi:10.1021/acssynbio.5b00100 · Cited by 104

Role of DNA sequence based structural features of promoters in transcription initiation and gene expression

Bansal, M., Kumar, A. A., & Yella, V. R. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.01.007 · Cited by 107

Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

Fang, L., Liu, S., Liu, M., Kang, X., Lin, S., Li, B., Connor, E. E., Baldwin, R. L., Tenesa, A., Ma, L., et al. (2019) · BMC Biology · doi:10.1186/s12915-019-0687-8 · Cited by 103

A recellularized human colon model identifies cancer driver genes

Chen, H. J., Wei, Z., Sun, J. M., Bhattacharya, A., Savage, D. J., Serda, R. E., Mackeyev, Y., Curley, S. A., Bu, P., Wang, L., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3586 · Cited by 99

A chromosome inversion near the KIT gene and the Tobiano spotting pattern in horses

Brooks, S. A., Lear, T. L., Adelson, D. L., & Bailey, E. (2007) · Cytogenetic and Genome Research · doi:10.1159/000112065 · Cited by 101

Moving beyond neurons: the role of cell type-specific gene regulation in Parkinson’s disease heritability

Reynolds, R. H., Botía, J. A., Nalls, M. A., Noyce, A. J., Nicolas, A., Cookson, M., Bandrés‐Ciga, S., Gibbs, J. R., Hernandez, D. G., Singleton, A., et al. (2019) · npj Parkinson s Disease · doi:10.1038/s41531-019-0076-6 · Cited by 101

Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods

Sun, F., Chronis, C., Kronenberg, M., Chen, X., Su, T., Lay, F. D., Plath, K., Kurdistani, S. K., & Carey, M. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.10.039 · Cited by 94

Characterization of Enhancer Function from Genome-Wide Analyses

Maston, G. A., Landt, S. G., Snyder, M. P., & Green, M. R. (2012) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090711-163723 · Cited by 105

Progress and challenges in bioinformatics approaches for enhancer identification

Kleftogiannis, D., Kalnis, P., & Bajić, V. B. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv101 · Cited by 92

Management of Gene Promoter Mutations in Molecular Diagnostics

de Vooght, K. M. K., van Wijk, R., & van Solinge, W. W. (2009) · Clinical Chemistry · doi:10.1373/clinchem.2008.120931 · Cited by 94

ChIA-PET analysis of transcriptional chromatin interactions

Zhang, J., Poh, H. M., Peh, S. Q., Sia, Y. Y., Li, G., Mulawadi, F. H., Goh, Y., Fullwood, M. J., Sung, W.-K. K., Ruan, X., et al. (2012) · Methods · doi:10.1016/j.ymeth.2012.08.009 · Cited by 96

Synthetic promoters capable of driving robust nuclear gene expression in the green alga Chlamydomonas reinhardtii

Scranton, M. A., Ostrand, J. T., Georgianna, D. R., Lofgren, S., Li, D. D., Ellis, R. C., Carruthers, D. N., Dräger, A., Masica, D. L., & Mayfield, S. P. (2016) · Algal Research · doi:10.1016/j.algal.2016.02.011 · Cited by 93

Clinical, Histopathological, and Molecular Diagnostics in Lethal Lung Developmental Disorders

Vincent, M., Karolak, J. A., Deutsch, G. H., Gambin, T., Popek, E. J., Isidor, B., Szafrański, P., Caignec, C. L., & Stankiewicz, P. (2019) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201903-0495tr · Cited by 92

Emergence of the Noncoding Cancer Genome: A Target of Genetic and Epigenetic Alterations

Zhou, S., Treloar, A. E., & Lupien, M. (2016) · Cancer Discovery · doi:10.1158/2159-8290.cd-16-0745 · Cited by 89

Detailing regulatory networks through large scale data integration

Huttenhower, C., Mutungu, K. T., Indik, N., Yang, W., Schroeder, M., Forman, J. J., Troyanskaya, O. G., & Coller, H. A. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp588 · Cited by 90

Identifying regulatory elements in eukaryotic genomes

Narlikar, L., & Ovcharenko, I. (2009) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/elp014 · Cited by 122

Toward a comprehensive catalog of regulatory elements

Fan, K., Pfister, E. L., & Weng, Z. (2023) · Human Genetics · doi:10.1007/s00439-023-02519-3 · Cited by 19

Finding distal regulatory elements in the human genome

Heintzman, N. D., & Ren, B. (2009) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2009.09.006 · Cited by 241

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 170

Transcriptional Regulatory Elements

Otto, W. (2011) · Cited by 3