Discovering sequences with potential regulatory characteristics

Genomics

Volumn 93, Issue 4, 2009, Pages 314-322

  Bina, Minou ^a   Wyss, Phillip ^a   Lazarus, Sheryl A ^a   Shah, Syed R ^a   Ren, Wenhui ^b   Szpankowski, Wojciech ^b   Crawford, Gregory E ^c   Park, Sang P ^b   Song, Xiaohui C ^b  

^a PURDUE UNIVERSITY   (United States)

^b Purdue University   (United States)

^c DUKE UNIVERSITY   (United States)

Author keywords

Codes in human DNA; Gene regulation; Genetic vocabulary; Human genome; Regulatory signals; Sequence context; Transcription factor binding sites

Indexed keywords

DEOXYRIBONUCLEASE I; GENOMIC DNA;

ARTICLE; BINDING SITE; CHROMOSOME 7; COMPUTER MODEL; DNA SEQUENCE; GENE CONTROL; GENE LOCUS; HUMAN; HUMAN GENOME; PREDICTION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; SIGNAL TRANSDUCTION;

BINDING SITES; CHROMOSOMES, HUMAN, PAIR 7; COMPUTATIONAL BIOLOGY; DNA; GENOME, HUMAN; HOMEODOMAIN PROTEINS; HUMANS; PROMOTER REGIONS, GENETIC; REGULATORY SEQUENCES, NUCLEIC ACID;

EID: 61849111746     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2008.11.008     Document Type: Article

References (50)

1. Searls D.B. The language of genes. Nature 420 (2002) 211-217
2. Collins F.S., Green E.D., Guttmacher A.E., and Guyer M.S. A vision for the future of genomics research. Nature 422 (2003) 835-847
3. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431 (2004) 931-945
4. Gamow G., and Ycas M. Statistical correlation of protein and ribonucleic acid composition. Proc. Natl. Acad. Sci. U. S. A. 41 (1955) 1011-1019
5. Crick F.H., Griffith J.S., and Orgel L.E. Codes without commas. Proc. Natl. Acad. Sci. U. S. A. 43 (1957) 416-421
6. Itzkovitz S., and Alon U. The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res. 17 (2007) 405-412
7. Bollenbach T., Vetsigian K., and Kishony R. Evolution and multilevel optimization of the genetic code. Genome Res. 17 (2007) 401-404
8. Levine M., and Tjian R. Transcription regulation and animal diversity. Nature 424 (2003) 147-151
9. Barbic A., Zimmer D.P., and Crothers D.M. Structural origins of adenine-tract bending. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 2369-2373
10. Schaefer C.B., Ooi S.K., Bestor T.H., and Bourc'his D. Epigenetic decisions in mammalian germ cells. Science 316 (2007) 398-399
11. Suzuki M.M., and Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet. 9 (2008) 465-476
12. Wu C. The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 286 (1980) 854-860
13. Elgin S.C. DNAase I-hypersensitive sites of chromatin. Cell 27 (1981) 413-415
14. Gross D.S., and Garrard W.T. Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57 (1988) 159-197
15. ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 (2007) 799-816
16. Crowley E.M., Roeder K., and Bina M. A statistical model for locating regulatory regions in genomic DNA. J. Mol. Biol. 268 (1997) 8-14
17. Crowley E.M. A Bayesian method for finding regulatory segments in DNA. Biopolymers 58 (2001) 165-174
18. Papatsenko D., and Levine M. Computational identification of regulatory DNAs underlying animal development. Nat. Methods 2 (2005) 529-534
19. Pennacchio L.A., and Rubin E.M. Genomic strategies to identify mammalian regulatory sequences. Nat. Rev. Genet. 2 (2001) 100-109
20. King D.C., Taylor J., Elnitski L., Chiaromonte F., Miller W., and Hardison R.C. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res. 15 (2005) 1051-1060
21. Pennacchio L.A., Ahituv N., Moses A.M., Prabhakar S., Nobrega M.A., Shoukry M., Minovitsky S., Dubchak I., Holt A., Lewis K.D., Plajzer-Frick I., Akiyama J., De Val S., Afzal V., Black B.L., Couronne O., Eisen M.B., Visel A., and Rubin E.M. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444 (2006) 499-502
22. Bina M., Wyss P., Ren W., Szpankowski W., Thomas E., Randhawa R., Reddy S., John P.M., Pares-Matos E.I., Stein A., Xu H., and Lazarus S.A. Exploring the characteristics of sequence elements in proximal promoters of human genes. Genomics 84 (2004) 929-940
23. Pares-Matos E.I., Milligan J.S., and Bina M. Exploring transcription factor binding properties of several non-coding DNA sequence elements in the human NF-IL6 gene. J. Mol. Biol. 357 (2006) 732-747
24. Hutchinson G.B. The prediction of vertebrate promoter regions using differential hexamer frequency analysis. Comput. Appl. Biosci. 12 (1996) 391-398
25. Wirth T., and Baltimore D. Nuclear factor NF-kappa B can interact functionally with its cognate binding site to provide lymphoid-specific promoter function. EMBO J. 7 (1988) 3109-3113
26. Rorth P., Nerlov C., Blasi F., and Johnsen M. Transcription factor PEA3 participates in the induction of urokinase plasminogen activator transcription in murine keratinocytes stimulated with epidermal growth factor or phorbol-ester. Nucleic Acids Res. 18 (1990) 5009-5017
27. Richard S., and Zingg H.H. Identification of a retinoic acid response element in the human oxytocin promoter. J. Biol. Chem. 266 (1991) 21428-21433
28. Pruitt K.D., Tatusova T., and Maglott D.R. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 33 (2005) D501-D504
29. Elnitski L., Jin V.X., Farnham P.J., and Jones S.J. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res 16 (2006) 1455-1464
30. Xi H., Shulha H.P., Lin J.M., Vales T.R., Fu Y., Bodine D.M., McKay R.D., Chenoweth J.G., Tesar P.J., Furey T.S., Ren B., Weng Z., and Crawford G.E. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet. 3 (2007) e136
31. Sabo P.J., Kuehn M.S., Thurman R., Johnson B.E., Johnson E.M., Cao H., Yu M., Rosenzweig E., Goldy J., Haydock A., Weaver M., Shafer A., Lee K., Neri F., Humbert R., Singer M.A., Richmond T.A., Dorschner M.O., McArthur M., Hawrylycz M., Green R.D., Navas P.A., Noble W.S., and Stamatoyannopoulos J.A. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat. Methods 3 (2006) 511-518
32. Solan Z., Horn D., Ruppin E., and Edelman S. Unsupervised learning of natural languages. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 11629-11634
33. Segal L., Lapidot M., Solan Z., Ruppin E., Pilpel Y., and Horn D. Nucleotide variation of regulatory motifs may lead to distinct expression patterns. Bioinformatics 23 (2007) i440-i449
34. Bina M., Wyss P., and Shah S.R. A database of 9-mers from promoter regions of human protein-coding genes. Methods Mol. Biol. 338 (2006) 129-134
35. Sinha S., Adler A.S., Field Y., Chang H.Y., and Segal E. Systematic functional characterization of cis-regulatory motifs in human core promoters. Genome Res. 18 (2008) 477-488
36. Lemon B., and Tjian R. Orchestrated response: a symphony of transcription factors for gene control. Genes Dev. 14 (2000) 2551-2569
37. FitzGerald P.C., Shlyakhtenko A., Mir A.A., and Vinson C. Clustering of DNA sequences in human promoters. Genome Res. 14 (2004) 1562-1574
38. Marino-Ramirez L., Spouge J.L., Kanga G.C., and Landsman D. Statistical analysis of over-represented words in human promoter sequences. Nucleic Acids Res. 32 (2004) 949-958
39. Xie X., Mikkelsen T.S., Gnirke A., Lindblad-Toh K., Kellis M., and Lander E.S. Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 7145-7150
40. Prabhakar S., Noonan J.P., Paabo S., and Rubin E.M. Accelerated evolution of conserved noncoding sequences in humans. Science 314 (2006) 786
41. Liang H., Lin Y.S., and Li W.H. Fast evolution of core promoters in primate genomes. Mol. Biol. Evol. 25 (2008) 1239-1244
42. Rhesus Macaque Genome Sequencing and Analysis Consortium. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316 (2007) 222-234
43. Trinklein N.D., Aldred S.J., Saldanha A.J., and Myers R.M. Identification and functional analysis of human transcriptional promoters. Genome Res. 13 (2003) 308-312
44. Wyss P., Lazarus S.A., and Bina M. A program toolkit for the analysis of regulatory regions of genes. Methods Mol. Biol. 338 (2006) 135-152
45. Szpankowski W. Average Case Analysis of Algorithms on Sequences (2001), Wiley, New Yor
46. Sandelin A., and Wasserman W.W. Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J. Mol. Biol. 338 (2004) 207-215
47. Chvátal V. The tail of the hypergeometric distribution. Discrete Math. 25 (1979) 285-287
48. Karolchik D., Kuhn R.M., Baertsch R., Barber G.P., Clawson H., Diekhans M., Giardine B., Harte R.A., Hinrichs A.S., Hsu F., Kober K.M., Miller W., Pedersen J.S., Pohl A., Raney B.J., Rhead B., Rosenbloom K.R., Smith K.E., Stanke M., Thakkapallayil A., Trumbower H., Wang T., Zweig A.S., Haussler D., and Kent W.J. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res. 36 (2008) D773-D779
49. Hsu F., Kent W.J., Clawson H., Kuhn R.M., Diekhans M., and Haussler D. The UCSC known genes. Bioinformatics 22 (2006) 1036-1046
50. Siepel A., Bejerano G., Pedersen J.S., Hinrichs A.S., Hou M., Rosenbloom K., Clawson H., Spieth J., Hillier L.W., Richards S., Weinstock G.M., Wilson R.K., Gibbs R.A., Kent W.J., Miller W., and Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15 (2005) 1034-1050