BMB Reports

생화학분자생물학회 (Korean Society for Biochemistry and Molecular Biology)
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CONVIRT: A web-based tool for transcriptional regulatory site identification using a conserved virtual chromosome

  • 발행 : 2009.12.31
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초록

Techniques for analyzing protein-DNA interactions on a genome-wide scale have recently established regulatory roles for distal enhancers. However, the large sizes of higher eukaryotic genomes have made identification of these elements difficult. Information regarding sequence conservation, exon annotation and repetitive regions can be used to reduce the size of the search region. However, previously developed resources are inadequate for consolidating such information. CONVIRT is a web resource for the identification of transcription factor binding sites and also features comparative genomics. Genomic information on ortholog-independent conserved regions, exons, repeats and sequences is integrated into the virtual chromosome, and statistically over-represented single or combinations of transcription factor binding sites are sought. CONVIRT provides regulatory network analysis for several organisms with long promoter regions and permits inter-species genome alignments. CONVIRT is freely available at http://biosoft.kaist.ac.kr/convirt.

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참고문헌

  1. Bussemaker, H. J., Li, H. and Siggia, E. D. (2001) Regulatory element detection using correlation with expression. Nat. Genet. 27, 167-171 https://doi.org/10.1038/84792
  2. Carroll, J. S., Meyer, C. A., Song, J., Li, W., Geistlinger, T. R., Eeckhoute, J., Brodsky, A. S., Keeton, E. K., Fertuck, K. C., Hall, G. F., Wang, Q., Bekiranov, S., Sementchenko, V., Fox, E. A., Silver, P. A., Gingeras, T. R., Liu, X. S. and Brown, M. (2006) Genome-wide analysis of estrogen receptor binding sites. Nat. Genet. 38, 1289-1297 https://doi.org/10.1038/ng1901
  3. Du, R., An, X. R., Chen, Y. F. and Qin, J. (2007) Some motifs were important for myostatin transcriptional regulation in sheep (Ovis aries). J. Biochem. Mol. Biol. 40, 547-553 https://doi.org/10.5483/BMBRep.2007.40.4.547
  4. Karanam, S. and Moreno, C. S. (2004) CONFAC: automated application of comparative genomic promoter analysis to DNA microarray datasets. Nucleic. Acids. Res. 32, W475-484 https://doi.org/10.1093/nar/gkh353
  5. Loots, G. G. and Ovcharenko, I. (2004) rVISTA 2.0: evolutionary analysis of transcription factor binding sites. Nucleic. Acids. Res. 32, W217-221 https://doi.org/10.1093/nar/gkh383
  6. Berezikov, E., Guryev, V. and Cuppen, E. (2005) CONREAL web server: identification and visualization of conserved transcription factor binding sites. Nucleic. Acids. Res. 33, W447-450 https://doi.org/10.1093/nar/gki378
  7. Pennacchio, L. A., Loots, G. G., Nobrega, M. A. and Ovcharenko, I. (2007) Predicting tissue-specific enhancers in the human genome. Genome. Res. 17, 201-211 https://doi.org/10.1101/gr.5972507
  8. Beer, M. A. and Tavazoie, S. (2004) Predicting gene expression from sequence. Cell. 117, 185-198 https://doi.org/10.1016/S0092-8674(04)00304-6
  9. Kato, M., Hata, N., Banerjee, N., Futcher, B. and Zhang, M. Q. (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol. 5, R56 https://doi.org/10.1186/gb-2004-5-8-r56
  10. Ryu, T., Kim, Y., Kim, D. W. and Lee, D. (2007) Computational identification of combinatorial regulation and transcription factor binding sites. Biotechnol. Bioeng. 97, 1594-1602 https://doi.org/10.1002/bit.21354
  11. NCBI Homologene. [http://www.ncbi.nlm.nih.gov/sites/ entrez?db=homologene]
  12. Schwartz, S., Kent, W. J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R. C., Haussler, D. and Miller, W. (2003) Human-mouse alignments with BLASTZ. Genome Res. 13, 103-107 https://doi.org/10.1101/gr.809403
  13. Wang, T., Zeng, J., Lowe, C. B., Sellers, R. G., Salama, S. R., Yang, M., Burgess, S. M., Brachmann, R. K. and Haus Haussler, D. (2007) Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc. Natl. Acad. Sci. U.S.A. 104, 18613-18618 https://doi.org/10.1073/pnas.0703637104
  14. Polak, P. and Domany, E. (2006) Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. BMC Genomics. 7, 133 https://doi.org/10.1186/1471-2164-7-133
  15. Johnson, R., Gamblin, R. J., Ooi, L., Bruce, A. W., Donaldson, I. J., Westhead, D. R., Wood, I. C., Jackson, R. M. and Buckley, N. J. (2006) Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication. Nucleic. Acids. Res. 34, 3862-3877 https://doi.org/10.1093/nar/gkl525
  16. UCSC Genome Browser. [http://hgdownload.cse.ucsc.edu/downloads.html]
  17. Kent, W. J., Baertsch, R., Hinrichs, A., Miller, W. and Haussler, D. (2003) Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. U.S.A. 100, 11484-11489 https://doi.org/10.1073/pnas.1932072100
  18. Lenhard, B., Sandelin, A., Mendoza, L., Engstrom, P., Jareborg, N. and Wasserman, W. W. (2003) Identification of conserved regulatory elements by comparative genome analysis. J. Biol. 2, 13 https://doi.org/10.1186/1475-4924-2-13
  19. Wasserman, W. W. and Sandelin, A. (2004) Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet. 5, 276-287 https://doi.org/10.1038/nrg1315
  20. Wasserman, W. W. and Fickett, J. W. (1998) Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol. 278, 167-181 https://doi.org/10.1006/jmbi.1998.1700
  21. Matys, V., Fricke, E., Geffers, R., Gossling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A. E., Kel-Margoulis, O. V., Kloos, D. U., Land, S., Lewicki-Potapov, B., Michael, H., Munch, R., Reuter, I., Rotert, S., Saxel, H., Scheer, M., Thiele, S. and Wingender, E. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic. Acids. Res. 31, 374-378 https://doi.org/10.1093/nar/gkg108
  22. Osoegawa, K., Mammoser, A. G., Wu, C., Frengen, E., Zeng, C., Catanese, J. J. and de Jong, P. J. (2001) A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res. 11, 483-496 https://doi.org/10.1101/gr.169601
  23. Ponomareva, O. N., Rose, J. A., Lasarev, M., Rasey, J. and Turker, M. S. (2002) Tissue-specific deletion and discontinuous loss of heterozygosity are signatures for the mutagenic effects of ionizing radiation in solid tissues. Cancer Res. 62, 1518-1523
  24. Semina, E. V., Murray, J. C., Reiter, R., Hrstka, R. F. and Graw, J. (2000) Deletion in the promoter region and altered expression of Pitx3 homeobox gene in aphakia mice. Hum. Mol. Genet. 9, 1575-1585 https://doi.org/10.1093/hmg/9.11.1575
  25. Takada, H., Imoto, I., Tsuda, H., Nakanishi, Y., Sakakura, C., Mitsufuji, S., Hirohashi, S. and Inazawa, J. (2006) Genomic loss and epigenetic silencing of very-low-density lipoprotein receptor involved in gastric carcinogenesis. Oncogene. 25, 6554-6562 https://doi.org/10.1038/sj.onc.1209657
  26. Levy, S., Sutton, G., Ng, P. C., Feuk, L., Halpern, A. L., Walenz, B. P., Axelrod, N., Huang, J., Kirkness, E. F., Denisov, G., Lin, Y., MacDonald, J. R., Pang, A. W., Shago, M., Stockwell, T. B., Tsiamouri, A., Bafna, V., Bansal, V., Kravitz, S. A., Busam, D. A., Beeson, K. Y., McIntosh, T. C., Remington, K. A., Abril, J. F., Gill, J., Borman, J., Rogers, Y. H., Frazier, M. E., Scherer, S. W., Strausberg, R. L. and Venter, J. C. (2007) The diploid genome sequence of an individual human. PLoS. Biol. 5, e254 https://doi.org/10.1371/journal.pbio.0050254
  27. Smith, A. D., Sumazin, P. and Zhang, M. Q. (2007) Tissue-specific regulatory elements in mammalian promoters. Mol. Syst. Biol. 3, 73
  28. Michal, L., Mizrahi-Man, O. and Pilpel, Y. (2008) Functional characterization of variations on regulatory motifs. PLoS. Genet. 4, e1000018 https://doi.org/10.1371/journal.pgen.1000018
  29. Vega, V. B., Lin, C. Y., Lai, K. S., Kong, S. L., Xie, M., Su, X., Teh, H. F., Thomsen, J. S., Yeo, A. L., Sung, W. K., Bourque, G. and Liu, E. T. (2006) Multiplatform genomewide identification and modeling of functional human estrogen receptor binding sites. Genome. Biol. 7, R82 https://doi.org/10.1186/gb-2006-7-9-r82
  30. Kel, A. E., Gossling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O. V. and Wingender, E. (2003) MATCH:A tool for searching transcription factor binding sites in DNA sequences. Nucleic. Acids. Res. 31, 3576-3579 https://doi.org/10.1093/nar/gkg585
  31. Bedell, J. A., Korf, I. and Gish, W. (2000) MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics. 16, 1040-1041 https://doi.org/10.1093/bioinformatics/16.11.1040
  32. Ho Sui, S. J., Fulton, D. L., Arenillas, D. J., Kwon, A. T. and Wasserman, W. W. (2007) oPOSSUM: integrated tools for analysis of regulatory motif over-representation. Nucleic. Acids. Res. 35, W245-252 https://doi.org/10.1093/nar/gkm427
  33. Zhou, Y., Ferguson, J., Chang, J. T. and Kluger, Y. (2007) Inter- and intra-combinatorial regulation by transcription factors and microRNAs. BMC Genomics. 8, 396 https://doi.org/10.1186/1471-2164-8-396