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Journal of Biomedicine and Biotechnology
Volume 2006, Article ID 71753, 16 pages
http://dx.doi.org/10.1155/JBB/2006/71753
Research Article

L1 Antisense Promoter Drives Tissue-Specific Transcription of Human Genes

Department of Gene Technology, ITallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia

Received 26 July 2005; Revised 11 November 2005; Accepted 16 November 2005

Copyright © 2006 Kert Mätlik et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. P L Deininger and M A Batzer, “Mammalian retroelements,” Genome Research, vol. 12, no. 10, pp. 1455–1465, 2002. View at Publisher · View at Google Scholar
  2. H H Jr Kazazian, “Mobile elements: drivers of genome evolution,” Science, vol. 303, no. 5664, pp. 1626–1632, 2004. View at Publisher · View at Google Scholar
  3. V K Rakyan, M E Blewitt, R Druker, J I Preis, and E Whitelaw, “Metastable epialleles in mammals,” Trends in Genetics, vol. 18, no. 7, pp. 348–351, 2002. View at Publisher · View at Google Scholar
  4. L N van de Lagemaat, J-R Landry, D L Mager, and P Medstrand, “Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions,” Trends in Genetics, vol. 19, no. 10, pp. 530–536, 2003. View at Publisher · View at Google Scholar
  5. K Kashkush, M Feldman, and A A Levy, “Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat,” Nature Genetics, vol. 33, no. 1, pp. 102–106, 2003. View at Publisher · View at Google Scholar
  6. M Speek, “Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes,” Molecular and Cellular Biology, vol. 21, no. 6, pp. 1973–1985, 2001. View at Publisher · View at Google Scholar
  7. O Ferrigno, T Virolle, Z Djabari, J P Ortonne, R J White, and D Aberdam, “Transposable B2 SINE elements can provide mobile RNA polymerase II promoters,” Nature Genetics, vol. 28, no. 1, pp. 77–81, 2001. View at Publisher · View at Google Scholar
  8. E Whitelaw and D I Martin, “Retrotransposons as epigenetic mediators of phenotypic variation in mammals,” Nature Genetics, vol. 27, no. 4, pp. 361–365, 2001. View at Publisher · View at Google Scholar
  9. D M Duhl, H Vrieling, K A Miller, G L Wolff, and G S Barsh, “Neomorphic agouti mutations in obese yellow mice,” Nature Genetics, vol. 8, no. 1, pp. 59–65, 1994. View at Publisher · View at Google Scholar
  10. A M Schulte, S Lai, A Kurtz, F Czubayko, A T Riegel, and A Wellstein, “Human trophoblast and choriocarcinoma expression of the growth factor pleiotrophin attributable to germ-line insertion of an endogenous retrovirus,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 25, pp. 14759–14764, 1996. View at Publisher · View at Google Scholar
  11. P Medstrand, J-R Landry, and D L Mager, “Long terminal repeats are used as alternative promoters for the endothelin B receptor and apolipoprotein C-I genes in humans,” The Journal of Biological Chemistry, vol. 276, no. 3, pp. 1896–1903, 2001. View at Publisher · View at Google Scholar
  12. J-R Landry, A Rouhi, P Medstrand, and D L Mager, “The Opitz syndrome gene Mid1 is transcribed from a human endogenous retroviral promoter,” Molecular Biology and Evolution, vol. 19, no. 11, pp. 1934–1942, 2002. View at Google Scholar
  13. C A Dunn, P Medstrand, and D L Mager, “An endogenous retroviral long terminal repeat is the dominant promoter for human β1,3-galactosyltransferase 5 in the colon,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 22, pp. 12841–12846, 2003. View at Publisher · View at Google Scholar
  14. C A Dunn and D L Mager, “Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus,” BMC Genomics, vol. 6, no. 1, p. 47, 2005. View at Publisher · View at Google Scholar
  15. P Nigumann, K Redik, K Mätlik, and M Speek, “Many human genes are transcribed from the antisense promoter of L1 retrotransposon,” Genomics, vol. 79, no. 5, pp. 628–634, 2002. View at Publisher · View at Google Scholar
  16. S J Wheelan, D M Church, and J M Ostell, “Spidey: a tool for mRNA-to-genomic alignments,” Genome Research, vol. 11, no. 11, pp. 1952–1957, 2001. View at Google Scholar
  17. W J Kent, C W Sugnet, T S Furey et al., “The human genome browser at UCSC,” Genome Research, vol. 12, no. 6, pp. 996–1006, 2002. View at Publisher · View at Google Scholar
  18. S F Altschul, T L Madden, A A Schäffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997. View at Publisher · View at Google Scholar
  19. T A Tatusova and T L Madden, “BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences,” FEMS Microbiology Letters, vol. 174, no. 2, pp. 247–250, 1999. View at Publisher · View at Google Scholar
  20. Y Suzuki, R Yamashita, K Nakai, and S Sugano, “DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs,” Nucleic Acids Research, vol. 30, no. 1, pp. 328–331, 2002. View at Publisher · View at Google Scholar
  21. M G Reese, F H Eeckman, D Kulp, and D Haussler, “Improved splice site detection in Genie,” Journal of Computational Biology: A Journal of Computational Molecular Cell Biology, vol. 4, no. 3, pp. 311–323, 1997. View at Google Scholar
  22. S Brunak, J Engelbrecht, and S Knudsen, “Prediction of human mRNA donor and acceptor sites from the DNA sequence,” Journal of Molecular Biology, vol. 220, no. 1, pp. 49–65, 1991. View at Publisher · View at Google Scholar
  23. S E Fisher, I van Bakel, S E Lloyd, S H Pearce, R V Thakker, and I W Craig, “Cloning and characterization of CLCN5, the human kidney chloride channel gene implicated in Dent disease (an X-linked hereditary nephrolithiasis),” Genomics, vol. 29, no. 3, pp. 598–606, 1995. View at Publisher · View at Google Scholar
  24. M Park, M Dean, K Kaul, M J Braun, M A Gonda, and G Vande Woude, “Sequence of MET protooncogene cDNA has features characteristic of the tyrosine kinase family of growth-factor receptors,” Proceedings of the National Academy of Sciences of the United States of America, vol. 84, no. 18, pp. 6379–6383, 1987. View at Publisher · View at Google Scholar
  25. M Bernard, H Yoshioka, E Rodriguez et al., “Cloning and sequencing of pro-alpha 1 (XI) collagen cDNA demonstrates that type XI belongs to the fibrillar class of collagens and reveals that the expression of the gene is not restricted to cartilagenous tissue,” The Journal of Biological Chemistry, vol. 263, no. 32, pp. 17159–17166, 1988. View at Google Scholar
  26. R L Strausberg, E A Feingold, L H Grouse et al., “Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 26, pp. 16899–16903, 2002. View at Publisher · View at Google Scholar
  27. K D Pruitt and D R Maglott, “RefSeq and LocusLink: NCBI gene-centered resources,” Nucleic Acids Research, vol. 29, no. 1, pp. 137–140, 2001. View at Publisher · View at Google Scholar
  28. S J Wheelan, Y Aizawa, J S Han, and J D Boeke, “Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolution,” Genome Research, vol. 15, no. 8, pp. 1073–1078, 2005. View at Publisher · View at Google Scholar
  29. A F Smit, G Tóth, A D Riggs, and J Jurka, “Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences,” Journal of Molecular Biology, vol. 246, no. 3, pp. 401–417, 1995. View at Publisher · View at Google Scholar
  30. T K Chatterjee, Z Liu, and R A Fisher, “Human RGS6 gene structure, complex alternative splicing, and role of N terminus and G protein γ-subunit-like (GGL) domain in subcellular localization of RGS6 splice variants,” The Journal of Biological Chemistry, vol. 278, no. 32, pp. 30261–30271, 2003. View at Publisher · View at Google Scholar
  31. E S Lander, L M Linton, B Birren et al., “Initial sequencing and analysis of the human genome,” Nature, vol. 409, no. 6822, pp. 860–921, 2001. View at Publisher · View at Google Scholar
  32. A Piehler, W E Kaminski, J J Wenzel, T Langmann, and G Schmitz, “Molecular structure of a novel cholesterol-responsive A subclass ABC transporter, ABCA9,” Biochemical and Biophysical Research Communications, vol. 295, no. 2, pp. 408–416, 2002. View at Publisher · View at Google Scholar
  33. B Malnic, P A Godfrey, and L B Buck, “The human olfactory receptor gene family,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 8, pp. 2584–2589, 2004. View at Publisher · View at Google Scholar
  34. J S Myers, B J Vincent, H Udall et al., “A comprehensive analysis of recently integrated human Ta L1 elements,” The American Journal of Human Genetics, vol. 71, no. 2, pp. 312–326, 2002. View at Publisher · View at Google Scholar
  35. A V Furano, D D Duvernell, and S Boissinot, “L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish,” Trends in Genetics, vol. 20, no. 1, pp. 9–14, 2004. View at Publisher · View at Google Scholar
  36. E A Bennett, L E Coleman, C Tsui, W S Pittard, and S E Devine, “Natural genetic variation caused by transposable elements in humans,” Genetics, vol. 168, no. 2, pp. 933–951, 2004. View at Publisher · View at Google Scholar
  37. K Maruyama and S Sugano, “Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides,” Gene, vol. 138, no. 1-2, pp. 171–174, 1994. View at Publisher · View at Google Scholar
  38. D L Spector, “The dynamics of chromosome organization and gene regulation,” Annual Review of Biochemistry, vol. 72, pp. 573–608, 2003. View at Publisher · View at Google Scholar
  39. Y Wang, D C Newton, G B Robb et al., “RNA diversity has profound effects on the translation of neuronal nitric oxide synthase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 21, pp. 12150–12155, 1999. View at Publisher · View at Google Scholar
  40. M Kozak, “Pushing the limits of the scanning mechanism for initiation of translation,” Gene, vol. 299, no. 1-2, pp. 1–34, 2002. View at Publisher · View at Google Scholar
  41. J-R Landry, D L Mager, and B T Wilhelm, “Complex controls: the role of alternative promoters in mammalian genomes,” Trends in Genetics, vol. 19, no. 11, pp. 640–648, 2003. View at Publisher · View at Google Scholar
  42. S K Eszterhas, E E Bouhassira, D I Martin, and S Fiering, “Transcriptional interference by independently regulated genes occurs in any relative arrangement of the genes and is influenced by chromosomal integration position,” Molecular and Cellular Biology, vol. 22, no. 2, pp. 469–479, 2002. View at Publisher · View at Google Scholar
  43. E M Prescott and N J Proudfoot, “Transcriptional collision between convergent genes in budding yeast,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 13, pp. 8796–8801, 2002. View at Publisher · View at Google Scholar
  44. M T McManus and P A Sharp, “Gene silencing in mammals by small interfering RNAs,” Nature Reviews. Genetics, vol. 3, no. 10, pp. 737–747, 2002. View at Publisher · View at Google Scholar