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For: Gershenzon NI, Ioshikhes IP. Synergy of human Pol II core promoter elements revealed by statistical sequence analysis. Bioinformatics 2004;21:1295-300. [PMID: 15572469 DOI: 10.1093/bioinformatics/bti172] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
51
Sugihara F, Kasahara K, Kokubo T. Highly redundant function of multiple AT-rich sequences as core promoter elements in the TATA-less RPS5 promoter of Saccharomyces cerevisiae. Nucleic Acids Res 2010;39:59-75. [PMID: 20805245 PMCID: PMC3017598 DOI: 10.1093/nar/gkq741] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
52
Warnatz HJ, Querfurth R, Guerasimova A, Cheng X, Haas SA, Hufton AL, Manke T, Vanhecke D, Nietfeld W, Vingron M, Janitz M, Lehrach H, Yaspo ML. Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. Nucleic Acids Res 2010;38:6112-23. [PMID: 20494980 PMCID: PMC2952857 DOI: 10.1093/nar/gkq402] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
53
Walker DJ, Suetterlin P, Reisenberg M, Williams G, Doherty P. Down-regulation of diacylglycerol lipase-alpha during neural stem cell differentiation: identification of elements that regulate transcription. J Neurosci Res 2010;88:735-45. [PMID: 19798744 DOI: 10.1002/jnr.22251] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
54
Albert TK, Grote K, Boeing S, Meisterernst M. Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells. Genome Biol 2010;11:R33. [PMID: 20230619 PMCID: PMC2864573 DOI: 10.1186/gb-2010-11-3-r33] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2009] [Revised: 02/22/2010] [Accepted: 03/15/2010] [Indexed: 11/10/2022]  Open
55
Riethoven JJM. Regulatory regions in DNA: promoters, enhancers, silencers, and insulators. Methods Mol Biol 2010;674:33-42. [PMID: 20827584 DOI: 10.1007/978-1-60761-854-6_3] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
56
Characterization of The Promoter Region and Upstream Regulation Region of Human and Mouse SCN3A Gene*. PROG BIOCHEM BIOPHYS 2009. [DOI: 10.3724/sp.j.1206.2008.00450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
57
Gazit K, Moshonov S, Elfakess R, Sharon M, Mengus G, Davidson I, Dikstein R. TAF4/4b x TAF12 displays a unique mode of DNA binding and is required for core promoter function of a subset of genes. J Biol Chem 2009;284:26286-96. [PMID: 19635797 DOI: 10.1074/jbc.m109.011486] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
58
Zeng J, Zhu S, Yan H. Towards accurate human promoter recognition: a review of currently used sequence features and classification methods. Brief Bioinform 2009;10:498-508. [PMID: 19531545 DOI: 10.1093/bib/bbp027] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
59
Pitulescu ME, Teichmann M, Luo L, Kessel M. TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulation. BMC BIOCHEMISTRY 2009;10:16. [PMID: 19515240 PMCID: PMC2702275 DOI: 10.1186/1471-2091-10-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Accepted: 06/10/2009] [Indexed: 12/20/2022]
60
Savinkova LK, Ponomarenko MP, Ponomarenko PM, Drachkova IA, Lysova MV, Arshinova TV, Kolchanov NA. TATA box polymorphisms in human gene promoters and associated hereditary pathologies. BIOCHEMISTRY (MOSCOW) 2009;74:117-29. [PMID: 19267666 DOI: 10.1134/s0006297909020011] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
61
Yarden G, Elfakess R, Gazit K, Dikstein R. Characterization of sINR, a strict version of the Initiator core promoter element. Nucleic Acids Res 2009;37:4234-46. [PMID: 19443449 PMCID: PMC2715227 DOI: 10.1093/nar/gkp315] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
62
Ozsolak F, Poling LL, Wang Z, Liu H, Liu XS, Roeder RG, Zhang X, Song JS, Fisher DE. Chromatin structure analyses identify miRNA promoters. Genes Dev 2009;22:3172-83. [PMID: 19056895 DOI: 10.1101/gad.1706508] [Citation(s) in RCA: 488] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
63
Distinct modes of gene regulation by a cell-specific transcriptional activator. Proc Natl Acad Sci U S A 2009;106:4213-8. [PMID: 19251649 DOI: 10.1073/pnas.0808347106] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
64
TFIIB recognition elements control the TFIIA-NC2 axis in transcriptional regulation. Mol Cell Biol 2008;29:1389-400. [PMID: 19114554 DOI: 10.1128/mcb.01346-08] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
65
Brick K, Watanabe J, Pizzi E. Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum. Genome Biol 2008;9:R178. [PMID: 19094208 PMCID: PMC2646282 DOI: 10.1186/gb-2008-9-12-r178] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 11/03/2008] [Accepted: 12/18/2008] [Indexed: 11/23/2022]  Open
66
Anwar F, Baker SM, Jabid T, Mehedi Hasan M, Shoyaib M, Khan H, Walshe R. Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach. BMC Bioinformatics 2008;9:414. [PMID: 18834544 PMCID: PMC2575220 DOI: 10.1186/1471-2105-9-414] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Accepted: 10/04/2008] [Indexed: 01/03/2023]  Open
67
Juven-Gershon T, Hsu JY, Theisen JW, Kadonaga JT. The RNA polymerase II core promoter - the gateway to transcription. Curr Opin Cell Biol 2008;20:253-9. [PMID: 18436437 DOI: 10.1016/j.ceb.2008.03.003] [Citation(s) in RCA: 269] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Accepted: 03/11/2008] [Indexed: 10/22/2022]
68
Maston GA, Evans SK, Green MR. Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet 2008;7:29-59. [PMID: 16719718 DOI: 10.1146/annurev.genom.7.080505.115623] [Citation(s) in RCA: 567] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
69
Profiling the thermodynamic softness of adenoviral promoters. Biophys J 2008;95:597-608. [PMID: 18390611 DOI: 10.1529/biophysj.107.123471] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
70
Moshonov S, Elfakess R, Golan-Mashiach M, Sinvani H, Dikstein R. Links between core promoter and basic gene features influence gene expression. BMC Genomics 2008;9:92. [PMID: 18298820 PMCID: PMC2279122 DOI: 10.1186/1471-2164-9-92] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 02/25/2008] [Indexed: 11/10/2022]  Open
71
Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, Sandelin A. A code for transcription initiation in mammalian genomes. Genes Dev 2008;18:1-12. [PMID: 18032727 PMCID: PMC2134772 DOI: 10.1101/gr.6831208] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2007] [Accepted: 10/14/2007] [Indexed: 11/24/2022]
72
DNA sequence and structural properties as predictors of human and mouse promoters. Gene 2007;410:165-76. [PMID: 18234453 PMCID: PMC2672154 DOI: 10.1016/j.gene.2007.12.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 11/30/2007] [Accepted: 12/05/2007] [Indexed: 11/21/2022]
73
Diss JKJ, Calissano M, Gascoyne D, Djamgoz MBA, Latchman DS. Identification and characterization of the promoter region of the Nav1.7 voltage-gated sodium channel gene (SCN9A). Mol Cell Neurosci 2007;37:537-47. [PMID: 18249135 DOI: 10.1016/j.mcn.2007.12.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 11/15/2007] [Accepted: 12/06/2007] [Indexed: 12/19/2022]  Open
74
Isogai Y, Keles S, Prestel M, Hochheimer A, Tjian R. Transcription of histone gene cluster by differential core-promoter factors. Genes Dev 2007;21:2936-49. [PMID: 17978101 PMCID: PMC2049195 DOI: 10.1101/gad.1608807] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Accepted: 09/21/2007] [Indexed: 12/16/2022]
75
Zhao X, Xuan Z, Zhang MQ. Boosting with stumps for predicting transcription start sites. Genome Biol 2007;8:R17. [PMID: 17274821 PMCID: PMC1852414 DOI: 10.1186/gb-2007-8-2-r17] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Revised: 12/01/2006] [Accepted: 02/02/2007] [Indexed: 12/05/2022]  Open
76
Deng W, Roberts SGE. TFIIB and the regulation of transcription by RNA polymerase II. Chromosoma 2007;116:417-29. [PMID: 17593382 DOI: 10.1007/s00412-007-0113-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Revised: 05/21/2007] [Accepted: 05/21/2007] [Indexed: 02/01/2023]
77
Malecová B, Gross P, Boyer-Guittaut M, Yavuz S, Oelgeschläger T. The initiator core promoter element antagonizes repression of TATA-directed transcription by negative cofactor NC2. J Biol Chem 2007;282:24767-76. [PMID: 17584739 DOI: 10.1074/jbc.m702776200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
78
Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume DA. Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet 2007;8:424-36. [PMID: 17486122 DOI: 10.1038/nrg2026] [Citation(s) in RCA: 367] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
79
Vardhanabhuti S, Wang J, Hannenhalli S. Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acids Res 2007;35:3203-13. [PMID: 17452354 PMCID: PMC1904283 DOI: 10.1093/nar/gkm201] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
80
Juven-Gershon T, Hsu JY, Kadonaga JT. Perspectives on the RNA polymerase II core promoter. Biochem Soc Trans 2007;34:1047-50. [PMID: 17073747 DOI: 10.1042/bst0341047] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
81
Deng W, Roberts SGE. Core promoter elements recognized by transcription factor IIB. Biochem Soc Trans 2007;34:1051-3. [PMID: 17073748 DOI: 10.1042/bst0341051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
82
Juven-Gershon T, Cheng S, Kadonaga JT. Rational design of a super core promoter that enhances gene expression. Nat Methods 2007;3:917-22. [PMID: 17124735 DOI: 10.1038/nmeth937] [Citation(s) in RCA: 157] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
83
Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves. BMC Bioinformatics 2006;7:522. [PMID: 17137509 PMCID: PMC1698937 DOI: 10.1186/1471-2105-7-522] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Accepted: 11/30/2006] [Indexed: 11/24/2022]  Open
84
Yang C, Bolotin E, Jiang T, Sladek FM, Martinez E. Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene 2006;389:52-65. [PMID: 17123746 PMCID: PMC1955227 DOI: 10.1016/j.gene.2006.09.029] [Citation(s) in RCA: 256] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2006] [Revised: 09/12/2006] [Accepted: 09/22/2006] [Indexed: 10/24/2022]
85
Thomas MC, Chiang CM. The general transcription machinery and general cofactors. Crit Rev Biochem Mol Biol 2006;41:105-78. [PMID: 16858867 DOI: 10.1080/10409230600648736] [Citation(s) in RCA: 615] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
86
Stewart JJ, Fischbeck JA, Chen X, Stargell LA. Non-optimal TATA Elements Exhibit Diverse Mechanistic Consequences. J Biol Chem 2006;281:22665-73. [PMID: 16772290 DOI: 10.1074/jbc.m603237200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
87
Luo Q, Yang W, Liu P. Promoter recognition based on the Interpolated Markov Chains optimized via simulated annealing and genetic algorithm. Pattern Recognit Lett 2006. [DOI: 10.1016/j.patrec.2005.11.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
88
Gershenzon NI, Trifonov EN, Ioshikhes IP. The features of Drosophila core promoters revealed by statistical analysis. BMC Genomics 2006;7:161. [PMID: 16790048 PMCID: PMC1538597 DOI: 10.1186/1471-2164-7-161] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Accepted: 06/21/2006] [Indexed: 11/19/2022]  Open
89
Jin VX, Singer GAC, Agosto-Pérez FJ, Liyanarachchi S, Davuluri RV. Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. BMC Bioinformatics 2006;7:114. [PMID: 16522199 PMCID: PMC1475891 DOI: 10.1186/1471-2105-7-114] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Accepted: 03/07/2006] [Indexed: 01/20/2023]  Open
90
Lee DH, Gershenzon N, Gupta M, Ioshikhes IP, Reinberg D, Lewis BA. Functional characterization of core promoter elements: the downstream core element is recognized by TAF1. Mol Cell Biol 2005;25:9674-86. [PMID: 16227614 PMCID: PMC1265815 DOI: 10.1128/mcb.25.21.9674-9686.2005] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
91
Buckland PR. The importance and identification of regulatory polymorphisms and their mechanisms of action. Biochim Biophys Acta Mol Basis Dis 2005;1762:17-28. [PMID: 16297602 DOI: 10.1016/j.bbadis.2005.10.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Revised: 10/11/2005] [Accepted: 10/11/2005] [Indexed: 01/16/2023]
92
Gershenzon NI, Stormo GD, Ioshikhes IP. Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites. Nucleic Acids Res 2005;33:2290-301. [PMID: 15849315 PMCID: PMC1084321 DOI: 10.1093/nar/gki519] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
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