Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  McNutt, Markey C ^a,b   Tongbai, Ron ^a   Cui, Wenwu ^a   Collins, Irene ^a   Freebern, Wendy J ^a,c   Montano, Idalia ^a   Haggerty, Cynthia M ^a   Chandramouli, G V R ^a   Gardner, Kevin ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^c BRISTOL MYERS SQUIBB COMPANY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL FUNCTIONS; CELLULAR FUNCTION; CIS-REGULATORY ELEMENTS; GENE EXPRESSION DATA; GENE ONTOLOGY TERMS; GENOMIC COMPOSITION; PARTITIONAL CLUSTERING; TRANSCRIPTION FACTOR BINDING SITES;

BINDING SITES; TRANSCRIPTION; TRANSCRIPTION FACTORS;

GENES;

5' UNTRANSLATED REGION; ARTICLE; BASE PAIRING; BINDING SITE; BIOINFORMATICS; COMPUTER PROGRAM; CORRELATION ANALYSIS; DATA ANALYSIS; DOWNSTREAM PROCESSING; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE LOCATION; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC TRANSCRIPTION; INFORMATION RETRIEVAL; INTERNET; PROMOTER REGION; PROTEIN BINDING; CELL FUNCTION; GENE EXPRESSION; GENETICS; HUMAN; METABOLISM; NOMENCLATURE; PHYSIOLOGY;

TRANSCRIPTION FACTOR;

BINDING SITES; CELL PHYSIOLOGICAL PHENOMENA; GENE EXPRESSION; HUMANS; PROMOTER REGIONS, GENETIC; TERMINOLOGY AS TOPIC; TRANSCRIPTION FACTORS;

EID: 27744546533     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-259     Document Type: Article

References (56)

1. Michelson AM: Deciphering genetic regulatory codes: a challenge for functional genomics. Proc Natl Acad Sci U S A 2002, 99: 546-548.
2. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW et al.: Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431: 99-104.
3. Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, Liu XS: A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Res 2004, 32: W204-W207.
4. Liu XS, Brutlag DL, Liu JS: An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol 2002, 20: 835-839.
5. Quandt K, Frech K, Karas H, Wingender E, Werner T: MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res 1995, 23: 4878-4884.
6. Hochheimer A, Tjian R: Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression. Genes Dev 2003, 17: 1309-1320.
7. Fan J, Yang X, Wang W, Wood WH, III, Becker KG, Gorospe M: Global analysis of stress-regulated mRNA turnover by using cDNA arrays. Proc Natl Acad Sci U S A 2002, 99: 10611-10616.
8. Schones DE, Sumazin P, Zhang MQ: Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics 2005, 21: 307-313.
9. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R et al.: The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004, 32: D258-D261.
10. Ashburner M, Mungall CJ, Lewis SE: Ontologies for biologists: a community model for the annotation of genomic data. Cold Spring Harb Symp Quant Biol 2003, 68: 227-235.
11. Diehn M, Alizadeh AA, Rando OJ, Liu CL, Stankunas K, Botstein D et al.: Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation. Proc Natl Acad Sci U S A 2002, 99: 11796-11801.
12. Kane LP, Lin J, Weiss A: Signal transduction by the TCR for antigen. Curr Opin Immunol 2000, 12: 242-249.
13. Lin Z, Fillmore GC, Um TH, Elenitoba-Johnson KS, Lim MS: Comparative microarray analysis of gene expression during activation of human peripheral blood T cells and leukemic Jurkat T cells. Lab Invest 2003, 83: 765-776.
14. Smith JL, Freebern WJ, Collins I, De Siervi A, Montano I, Haggerty CM et al: Kinetic profiles of p300 occupancy in vivo predict common features of promoter structure and coactivator recruitment. Proc Natl Acad Sci U S A 2004, 101: 11554-11559.
15. Alter O, Brown PO, Botstein D: Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A 2000, 97: 10101-10106.
16. Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M et al: GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 2003, 4: R28.
17. Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB: Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol Biol 2003, 3: 19.
18. Hilger-Eversheim K, Moser M, Schorle H, Buettner R: Regulatory roles of AP-2 transcription factors in vertebrate development, apoptosis and cell-cycle control. Gene 2000, 260: 1-12.
19. Bar-Eli M: Gene regulation in melanoma progression by the AP-2 transcription factor. Pigment Cell Res 2001, 14: 78-85.
20. Benson LQ, Coon MR, Krueger LM, Han GC, Sarnaik AA, Wechsler DS: Expression of MXI1, a Myc antagonist, is regulated by Sp1 and AP2. J Biol Chem 1999, 274: 28794-28802.
21. Adamson E, de B, I, Mittal S, Wang Y, Hayakawa J, Korkmaz K et al: Egr1 signaling in prostate cancer. Cancer Biol Ther 2003, 2: 617-622.
22. Gaboli M, Kotsi PA, Gurrieri C, Cattoretti G, Ronchetti S, Cordon-Cardo C et al: Mzf1 controls cell proliferation and tumorigenesis. Genes Dev 2001, 15: 1625-1630.
23. Hromas R, Davis B, Rauscher FJ, III, Klemsz M, Tenen D, Hoffman S et al.: Hematopoietic transcriptional regulation by the myeloid zinc finger gene, MZF-1. Curr Top Microbiol Immunol 1996, 211: 159-164.
24. Lin A, Karin M: NF-kappaB in cancer: a marked target. Semin Cancer Biol 2003, 13: 107-114.
25. Copertino DW, Jenkinson S, Jones FS, Edelman GM: Structural and functional similarities between the promoters for mouse tenascin and chicken cytotactin. Proc Natl Acad Sci U S A 1995, 92: 2131-2135.
26. Iademarco MF, McQuillan JJ, Dean DC: Vascular cell adhesion molecule 1: contrasting transcriptional control mechanisms in muscle and endothelium. Proc Natl Acad Sci U S A 1993, 90: 3943-3947.
27. Greenbaum S, Zhuang Y: Regulation of early lymphocyte development by E2A family proteins. Semin Immunol 2002, 14: 405-414.
28. Genetta T, Ruezinsky D, Kadesch T: Displacement of an E-box-binding repressor by basic helix-loop-helix proteins: implications for B-cell specificity of the immunoglobulin heavy-chain enhancer. Mol Cell Biol 1994, 14: 6153-6163.
29. Postigo AA, Dean DC: Independent repressor domains in ZEB regulate muscle and T-cell differentiation. Mol Cell Biol 1999, 19: 7961-7971.
30. [http://genome.ucsc.edu]
31. Palaniswamy SK, Jin VX, Sun H, Davuluri RV: OMGProm: a database of orthologous mammalian gene promoters. Bioinformatics 2005, 21: 835-836.
32. Suzuki Y, Yamashita R, Nakai K, Sugano S: DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res 2002, 30: 328-331.
33. Landry JR, Mager DL, Wilhelm BT: Complex controls: the role of alternative promoters in mammalian genomes. Trends Genet 2003, 19: 640-648.
34. Levine M, Tjian R: Transcription regulation and animal diversity. Nature 2003, 424: 147-151.
35. Butler JE, Kadonaga JT: The RNA polymerase II core promoter: a key component in the regulation of gene expression. Genes Dev 2002, 16: 2583-2592.
36. Butler JE, Kadonaga JT: Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev 2001, 15: 2515-2519.
37. Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E et al.: Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 2005, 23: 137-144.
38. Serfling E, Avots A, Neumann M: The architecture of the interieukin-2 promoter: a reflection of T lymphocyte activation. Biochim Biophys Acta 1995, 1263: 181-200.
39. Shapiro VS, Truitt KE, Imboden JB, Weiss A: CD28 mediates transcriptional upregulation of the interleukin-2 (IL-2) promoter through a composite element containing the CD28RE and NF-IL-2B AP-1 sites. Mol Cell Biol 1997, 17: 4051-4058.
40. Butscher WG, Powers C, Olive M, Vinson C, Gardner K: Coordinate transactivation of the interleukin-2 CD28 response element by c-Rel and ATF-1/CREB2. J Biol Chem 1998, 273: 552-560.
41. Sun YL, Glimcher LH, Hoey T: Novel nfat sites that mediate activation of the interleukin-2 promoter in response to t-cell receptor stimulation. Mol Cell Biol 1995, 15: 6299-6310.
42. Powell JD, Lerner CG, Ewoldt GR, Schwartz RH: The -180 site of the IL-2 promoter is the target of CREB/CREM binding in T cell anergy. J Immunol 1999, 163: 6631-6639.
43. Rockman MV, Hahn MW, Soranzo N, Loisel DA, Goldstein DB, Wray GA: Positive selection on MMP3 regulation has shaped heart disease risk. Curr Biol 2004, 14: 1531-1539.
44. Phair RD, Misteli T: High mobility of proteins in the mammalian cell nucleus. Nature 2000, 404: 604-609.
45. Gardiner-Garden M, Frommer M: CpG islands in vertebrate genomes. J Mol Biol 1987, 196: 261-282.
46. Yamashita R, Suzuki Y, Sugano S, Nakai K: Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene 2005, 350: 129-136.
47. Stepanova M, Tiazhelova T, Skoblov M, Baranova A: A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas. Bioinformatics 2005, 21: 1789-1796.
48. Tullai JW, Schaffer ME, Mullenbrock S, Kasif S, Cooper GM: Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and MEK/ERK signaling pathways. J Biol Chem 2004, 279: 20167-20177.
49. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM: Systematic determination of genetic network architecture. Nat Genet 1999, 22: 281-285.
50. Bluthgen N, Kielbasa SM, Herzel H: Inferring combinatorial regulation of transcription in silico. Nucleic Acids Res 2005, 33: 272-279.
51. [http://prospector.nci.nih.gov]
52. [http://genome.nci.nih.gov/tools/promoall.html]
53. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R et al.: TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 2003, 31: 374-378.
54. Dougherty ER, Barrera J, Brun M, Kim S, Cesar RM, Chen Y et al.: Inference from clustering with application to gene-expression microarrays. J Comput Biol 2002, 9: 105-126.
55. Davies DL, Bouldin DW: A cluster separation measure. IEEE Transactions on Pattern Analysis and Machine Intelligence 1979, 1: 224-227.
56. [http://cran.r-project.org/]