Genomics & Informatics

Korea Genome Organization (한국유전체학회)
권호 표지

REPEATOME: A Database for Repeat Element Comparative Analysis in Human and Chimpanzee

  • Published : 2007.12.31
Download PDF
⟨ Previous Next ⟩

Abstract

An increasing number of primate genomes are being sequenced. A direct comparison of repeat elements in human genes and their corresponding chimpanzee orthologs will not only give information on their evolution, but also shed light on the major evolutionary events that shaped our species. We have developed REPEATOME to enable visualization and subsequent comparisons of human and chimpanzee repeat elements. REPEATOME (http://www.repeatome.org/) provides easy access to a complete repeat element map of the human genome, as well as repeat element-associated information. It provides a convenient and effective way to access the repeat elements within or spanning the functional regions in human and chimpanzee genome sequences. REPEATOME includes information to compare repeat elements and gene structures of human genes and their counterparts in chimpanzee. This database can be accessed using comparative search options such as intersection, union, and difference to find lineage-specific or common repeat elements. REPEATOME allows researchers to perform visualization and comparative analysis of repeat elements in human and chimpanzee.

Keywords

References

  1. Batzer, M. A., and Deininger, P. L. (2002). Alu repeats and human genomic diversity. Nat. Rev. Genet. 3, 370-379 https://doi.org/10.1038/nrg798
  2. Smit, A. F., Toth, G., Riggs, A. D., and Jurka, J. (1995). Ancestral mammalian-wide subfamilies of LINE 1 repetitive sequences. J. Mol. Biol. 246, 401-417 https://doi.org/10.1006/jmbi.1994.0095
  3. The Chimpanzee Sequencing and Analysis Consortium (2005). Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 437, 69-87 https://doi.org/10.1038/nature04072
  4. Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., and FitzHugh, W. et al. (2001). Initial sequencing and analysis of the human genome. Nature. 409, 860‐921
  5. Mills, R. E, Bennett, E. A., Iskow, R. C., Luttig, C. T., Tsui, C., Pittard, W. S., and Devine, S. E. (2006). Recently mobilized transposons in the human and chimpanzee genomes. Am. J. Hum. Genet. 78, 671-679 https://doi.org/10.1086/501028
  6. Ohno, S., and Yomo, T. (1991). The grammatical rule for all DNA: junk and coding sequences. Electrophoresis. 12, 103-108 https://doi.org/10.1002/elps.1150120203
  7. Dagan, T., Sorek, R., Sharon, E., Ast, G., and Graur, D. (2004). AluGene: a database of Alu elements incorporated within protein-coding genes. Nucleic Acids Res. 32, D489-D492 https://doi.org/10.1093/nar/gkh132
  8. Le Goff, W., Guerin, M., Chapman, M. J., and Thillet, J. (2003). A CYP7A promoter binding factor site and Alu repeat in the distal promoter region are implicated in regulation of human CETP gene expression. J. Lipid Res. 44, 902-910 https://doi.org/10.1194/jlr.M200423-JLR200
  9. Grover, D., Kannan, K., Brahmachari, S. K., and Mukerji, M. (2005). Alu-ring elements in the primate genomes. Genetica. 124, 273-289 https://doi.org/10.1007/s10709-005-3086-8
  10. Arnaud, P., Goubely, C., Pelissier, T., and Deragon, J. M. (2000). SINE retroposons can be used in vivo as nucleation centers for de novo methylation. Mol. Cell. Biol. 20, 3434-3441 https://doi.org/10.1128/MCB.20.10.3434-3441.2000
  11. Thornburg, B. G., Gotea, V., and Makalowski, W. (2006). Transposable elements as a significant source of transcription regulating signals. Gene. 365, 104-110 https://doi.org/10.1016/j.gene.2005.09.036
  12. Jurka, J., Kapitonov, V. V., Pavlicek, A., Klonowski, P., Kohany, O., and Walichiewicz, J. (2005). Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 110, 462-467 https://doi.org/10.1159/000084979
  13. Hinrichs, A. S., Karolchik, D., Baertsch, R., Barber, G. P., Bejerano, G., Clawson, H., Diekhans, M., Furey, T. S., Harte, R. A., Hsu, F., Hillman-Jackson, J., Kuhn, R. M., Pedersen, J. S., Pohl, A., Raney, B. J., Rosenbloom, K. R., Siepel, A., Smith, K. E., Sugnet, C. W., Sultan-Qurraie, A., Thomas, D. J., Trumbower, H., Weber, R. J., Weirauch, M., Zweig, A. S., Haussler, D., and Kent, W. J. (2006). The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 34, D590-D598 https://doi.org/10.1093/nar/gkj144
  14. Nagashima, T., Matsuda, H., Silva, D. G., Petrovsky, N., Konagaya, A., Schönbach, C., Kasukawa, T., Arakawa, T., Carninci, P., Kawai, J., and Hayashizaki, Y. (2004). FREP: a database of functional repeats in mouse cDNAs. Nucleic Acids Res. 32, D471‐D475 https://doi.org/10.1093/nar/gkh353
  15. Boby, T., Patch, A. M., and Aves, S. J. (2005). TRbase: a database relating tandem repeats to disease genes for the human genome. Bioinformatics. 21, 811-816 https://doi.org/10.1093/bioinformatics/bti059
  16. Pruitt, K. D., Tatusova, T., and Maglott, D. R. (2005). NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 33, D501-504 https://doi.org/10.1093/nar/gki476
  17. Kent, W. J. (2002). BLAT-the BLAST-like alignment tool. Genome Res. 12, 656‐664
  18. Maglott, D., Ostell, J., Pruitt, K. D., and Tatusova, T. (2005). Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 33, D54-D58 https://doi.org/10.1093/nar/gni052
  19. Matys, V., Kel-Margoulis, O. V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K., Voss, N., Stegmaier, P., Lewicki-Potapov, B., Saxel, H., Kel, A. E., and Wingender, E. (2006). TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34, D108-110 https://doi.org/10.1093/nar/gkj143
  20. Zhang, M. Q. (1998). Statistical features of human exons and their flanking regions. Hum. Mol. Genet. 7, 919-932 https://doi.org/10.1093/hmg/7.5.919
  21. Lambert, A., Fontaine, J. F., Legendre, M., Leclerc, F., Permal, E., Major, F., Putzer, H., Delfour, O., Michot, B., and Gautheret, D. (2004). The ERPIN server: an interface to profile-based RNA motif identification. Nucleic Acids Res. 32, W160-W165 https://doi.org/10.1093/nar/gkh418
  22. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2
  23. McEntyre, J., and Lipman, D. (2001). PubMed: bridging the information gap. CMAJ. 164, 1317-1319
  24. Woo, T., Kim, Y., Kwon, J., and Seo, J. (2007). RepWeb: A Web-Based Search Tool for Repeat-Related Literatures. Genomics & Informatics. 5, 89-91