Exploring the characteristics of sequence elements in proximal promoters of human genes

Genomics

Volumn 84, Issue 6, 2004, Pages 929-940

  Bina, Minou ^a   Wyss, Phillip ^a   Ren, Wenhui ^b   Szpankowski, Wojciech ^b   Thomas, Elizabeth ^c   Randhawa, Ranjit ^a   Reddy, Sreedeepti ^a   John, Priya M ^a   Pares Matos, Elsie I ^a   Stein, Arnold ^a   Xu, Hao ^a   Lazarus, Sheryl A ^a  

^a PURDUE UNIVERSITY   (United States)

^b Purdue University   (United States)

^c Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

Codes in human DNA; Gene regulation; Human genome; Sequence context of human genomic DNA; Transcription factor binding sites

Indexed keywords

CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; EARLY GROWTH RESPONSE FACTOR 1; GENOMIC DNA; STAT PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR SP1;

ARTICLE; BINDING SITE; CPG ISLAND; GENE CONTROL; GENE EXPRESSION; GENE IDENTIFICATION; GENE SEQUENCE; GENE TARGETING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN FAMILY; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; TRANSCRIPTION INITIATION SITE; VERTEBRATE;

5' UNTRANSLATED REGIONS; BASE SEQUENCE; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION REGULATION; HUMANS; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; RESPONSE ELEMENTS; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC;

VERTEBRATA;

EID: 7944234271     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ygeno.2004.08.013     Document Type: Article

References (50)

1. B. Lemon, and R. Tjian Orchestrated response: a symphony of transcription factors for gene control Genes Dev. 14 2000 2551 2569
2. International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome Nature (London) 409 2001 860 921
3. J.C. Venter The sequence of the human genome Science 291 2001 1304 1351
4. R.H. Waterston Initial sequencing and comparative analysis of the mouse genome Nature 420 2002 520 562
5. S.T. Smale, and J.T. Kadonaga The RNA polymerase II core promoter Annu. Rev. Biochem. 72 1999 449 479
6. E.M. Crowley, K. Roeder, and M. Bina A statistical model for locating regulatory regions in genomic DNA J. Mol. Biol. 268 1997 8 14
7. C.H. Yuh, H. Bolouri, and E.H. Davidson Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene Science 279 1998 1896 1902
8. E.M. Crowley A Bayesian method for finding regulatory segments in DNA Biopolymers 58 2001 165 174
9. B.P. Berman, Y. Nibu, B.D. Pfeiffer, P. Tomancak, S.E. Celniker, M. Levine, G.M. Rubin, and M.B. Eisen Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome Proc. Natl. Acad. Sci. USA 99 2002 757 762
10. M.C. Frith, J.L. Spouge, U. Hansen, and Z. Weng Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences Nucleic Acids Res. 30 2002 3214 3224
11. A.G. Jegga, S.P. Sherwood, J.W. Carman, A.T. Pinski, J.L. Phillips, J.P. Pestian, and B.J. Aronow Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes Genome Res. 12 2002 1408 1417
12. W.W. Wasserman, and J.W. Fickett Identification of regulatory regions which confer muscle-specific gene expression J. Mol. Biol. 278 1998 67 181
13. H.J. Bussemaker, H. Li, and E.D. Siggia Regulatory element detection using a probabilistic segmentation model Proc. Int. Conf. Intell. Syst. Mol. Biol. 8 2000 67 74
14. M. Kellis, N. Patterson, M. Endrizzi, B. Birren, and E.S. Lander Sequencing and comparison of yeast species to identify genes and regulatory elements Nature 423 2003 241 254
15. R. Liu, R.C. McEachin, and D.J. States Computationally identifying novel NF-kappa B-regulated immune genes in the human genome Genome Res. 13 2003 654 661
16. A.E. Kel, O.V. Kel-Margoulis, P.J. Farnham, S.M. Bartley, E. Wingender, and M.Q. Zhang Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors J. Mol. Biol. 309 2001 99 120
17. R. Hardison, and W. Miller Use of long sequence alignments to study the evolution and regulation of mammalian globin gene clusters Mol. Biol. Evol. 10 1993 73 102
18. G.B. Hutchinson The prediction of vertebrate promoter regions using differential hexamer frequency analysis Comput. Appl. Biosci. 12 1996 391 398
19. L. Marino-Ramirez, J.L. Spouge, G.C. Kanga, and D. Landsman Statistical analysis of over-represented words in human promoter sequences Nucleic Acids Res. 32 2004 949 958
20. N.D. Trinklein, S.J. Aldred, A.J. Saldanha, and R.M. Myers Identification and functional analysis of human transcriptional promoters Genome Res. 13 2003, 308 312
21. W.J. Kent, C.W. Sugnet, T.S. Furey, K.M. Roskin, T.H. Pringle, A.M. Zahler, and D. Haussler The human genome browser at UCSC Genome Res. 12 2002 996 1006
22. M. Regnier, and W. Szpankowski On pattern frequency occurrences in a Markovian sequence algorithmica 22 1998 631 649
23. W. Szpankowski Average Case Analysis of Algorithms on Sequences 2001 Wiley NewYork
24. M. Gardiner-Garden, and M. Frommer CpG islands in vertebrate genomes J. Mol. Biol. 196 1987 261 282
25. Y. Yang, E.I. Pares-Matos, V.M. Tesmer, C. Dai, S. Ashworth, J. Huai, and M. Bina Organization of the promoter region of the human NF-IL6 gene Biochim. Biophys. Acta 1577 2002 102 108
26. E.I. Pares-Matos, Regulation of Gene Expression by DNA-Protein and Protein-Protein Interactions, Purdue University, West Lafayette, IN, 2000. [Ph.D. thesis]
27. S. Okamoto, K. Sherman, G. Bai, and S.A. Lipton Effect of the ubiquitous transcription factors, SP1 and MAZ, on NMDA receptor subunit type 1 (NR1) expression during neuronal differentiation Brain Res. Mol. Brain Res. 107 2002 89 96
28. D. Macleod, J. Charlton, J. Mullins, and A.P. Bird Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island Genes Dev. 8 1994 2282 2292
29. V.A. Bernath, A.F. Muro, A.D. Vitullo, M.A. Bley, J.L. Baranao, and A.R. Kornblihtt Cyclic AMP inhibits fibronectin gene expression in a newly developed granulosa cell line by a mechanism that suppresses cAMP-responsive element-dependent transcriptional activation Biol. Chem. 265 1990 18219 18226
30. L. Guillemot, A. Levy, M. Raymondjean, and B. Rothhut Angiotensin II-induced transcriptional activation of the cyclin D1 gene is mediated by Egr-1 in CHO-AT(1A) cells J. Biol. Chem. 276 2001 39394 39403
31. M.R. Montminy, G.A. Gonzalez, and K.K. Yamamoto Regulation of cAMP-inducible genes by CREB Trends Neurosci. 13 1990 184 188
32. B.H. Lee, and M.B. Mathews Transcriptional coactivator cAMP response element binding protein mediates induction of the human proliferating cell nuclear antigen promoter by the adenovirus E1A oncoprotein Proc. Natl. Acad. Sci. USA 94 1997 4481 4486
33. T. Yoganathan, N.K. Bhat, and B.H. Sells A positive regulator of the ribosomal protein gene, beta factor, belongs to the ETS oncoprotein family Biochem. J. 287 1992 349 353
34. T. Hsu, M. Trojanowska, and D.K. Watson Ets proteins in biological control and cancer J. Cell. Biochem. 91 2004 896 903
35. E. Lelièvre, F. Lionneton, F. Soncin, and B. Vandenbunder The Ets family contains transcriptional activators and repressors involved in angiogenesis Int. J. Biochem. Cell Biol. 33 2001 391 407
36. P.A. Jones, and P.W. Laird Cancer epigenetics comes of age Nat. Genet. 21 1999 163 167
37. H. Maier, J. Colbert, D. Fitzsimmons, D.R. Clark, and J. Hagman Activation of the early B-cell-specific mb-1 (Ig-alpha) gene by Pax-5 is dependent on an unmethylated Ets binding site Mol. Cell Biol. 23 2003 1946 1960
38. K. Gaston, and M. Fried CpG methylation and the binding of YY1 and ETS proteins to the Surf-1/Surf-2 bidirectional promoter Gene 157 1995 257 259
39. B.E. Lonze, and D.D. Ginty Function and regulation of CREB family transcription factors in the nervous system Neuron 35 2002 605 623
40. U. Otten, P. Marz, K. Heese, C. Hock, D. Kunz, and S. Rose-John Cytokines and neurotrophins interact in normal and diseased states Ann. N. Y. Acad. Sci. 917 2000 322 330
41. D. De Cesare, G.M. Fimia, and P. Sassone-Corsi CREM, a master-switch of the transcriptional cascade in male germ cells J. Endocrinol. Invest. 23 2000 592 596
42. R.C. Iannello, J. Young, S. Sumarsono, M.J. Tymms, H.H. Dahl, J. Gould, M. Hedger, and I. Kola Regulation of Pdha-2 expression is mediated by proximal promoter sequences and CpG methylation Mol. Cell Biol. 17 1997 612 619
43. M. Bina, and E. Crowley Sequence patterns defining the 5′ boundary of human genes Biopolymers 59 2001 347 355
44. K. Hilger-Eversheim, M. Moser, H. Schorle, and R. Buettner Regulatory roles of AP-2 transcription factors in vertebrate development, apoptosis and cell-cycle control Gene 260 2000 1 12
45. F. Zhao, C.G. Weismann, M. Satoda, M.E. Pierpont, E. Sweeney, E.M. Thompson, and B.D. Gelb TFAP2B mutations that cause Char syndrome provide a genotype-phenotype correlation Am. J. Hum. Genet. 69 2001 695 703
46. M. Imagawa, R. Chiu, and M. Karin Transcription factor AP-2 mediates induction by two different signal-transduction pathways: protein kinase C and cAMP Cell 51 1987 251 260
47. K.J. O'Donovan, W.G. Tourtellotte, J. Millbrandt, and J.M. Baraban The EGR family of transcription-regulatory factors: progress at the interface of molecular and systems neuroscience Trends Neurosci. 22 1999 167 173
48. G. Thiel, and G. Cibelli Regulation of life and death by the zinc finger transcription factor Egr-1 J. Cell. Physiol. 193 2002 287 292
49. J. Jurka, P. Klonowski, V. Dagman, and P. Pelton CENSOR- a program for identification and elimination of repetitive elements from DNA sequences Comput. Chem. 20 1996 119 122
50. P. Jacquet, and W. Szpankowski Autocorrelation on words and its applications: analysis of suffix trees by string-ruler approach J. Comb. Theory Ser. A 66 1994 237 269