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The Identification of Antisense Gene Pairs Through Available Software

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Bioinformatics Research and Applications (ISBRA 2007)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4463))

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Abstract

Antisense genes have been shown to have a variety of functions in both prokaryotes and recently in eukaryotes as well. They are hypothesized to be an important part of every genome and have been shown to be evolutionarily conserved as well. Naturally, it is in our interest to develop a software for identifying antisense pairs. While a variety of approaches and software do exist, each approach has its limitations and the software is not meant for large-scale analyses for identifying both cis and trans antisense genes. Here we present a novel way to identify antisense genes and show the results we obtained through it. While in no means a perfect solution, we do manage to show a possible way that may lead to more accurate prediction of antisense genes.

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References

  1. Munroe, S.H., Zhu, J.: Overlapping transcripts, double-stranded RNA and antisense regulation: A genomic perspective. Cellular and Molecular Life Sciences 63(18), 2102–2118 (2006)

    Article  Google Scholar 

  2. Yelin, R., et al.: Widespread occurrence of antisense transcription in the human genome. Nature Biotechnology 21(4), 379–386 (2003)

    Article  Google Scholar 

  3. Kiyosawa, H., et al.: Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Research 13(6B), 1324–1334 (2003)

    Google Scholar 

  4. Katayama, S., et al.: Antisense transcription in the mammalian transcriptome. Science 309(5740), 1564–1566 (2005)

    Article  Google Scholar 

  5. Chen, J.J., et al.: Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Research 32(16), 4812–4820 (2004)

    Article  Google Scholar 

  6. Wang, X.J., Gaasterland, T., Chua, N.H.: Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biology 6(4) (2005)

    Google Scholar 

  7. Wang, H., Chua, N.-H., Wang, X.-J.: Prediction of trans-antisense transcripts in Arabidopsis thaliana. Genome Biology, 7(10), R92 (2006)

    Google Scholar 

  8. Rosok, O., Sioud, M.: Systematic identification of sense-antisense transcripts in mammalian cells. Nature Biotechnology 22(1), 104–108 (2004)

    Article  Google Scholar 

  9. Dahary, D., Elroy-Stein, O., Sorek, R.: Naturally occurring antisense: Transcriptional leakage or real overlap? Genome Research 15(3), 364–368 (2005)

    Article  Google Scholar 

  10. Lavorgna, G., et al.: In search of antisense. Trends in Biochemical Sciences 29(2), 88–94 (2004)

    Article  Google Scholar 

  11. Makalowska, I., Lin, C.F., Makalowski, W.: Overlapping genes in vertebrate genomes. Computational Biology and Chemistry 29(1), 1–12 (2005)

    Article  MATH  Google Scholar 

  12. Knee, R., Murphy, P.R.: Regulation of gene expression by natural antisense RNA transcripts. Neurochemistry International 31(3), 379–392 (1997)

    Article  Google Scholar 

  13. Farrell, C.M., Lukens, L.N.: Naturally-Occurring Antisense Transcripts Are Present in Chick-Embryo Chondrocytes Simultaneously with the down-Regulation of the Alpha-1(I) Collagen Gene. Journal of Biological Chemistry 270(7), 3400–3408 (1995)

    Article  Google Scholar 

  14. Prescott, E.M., Proudfoot, N.J.: Transcriptional collision between convergent genes in budding yeast. Proceedings of the National Academy of Sciences of the United States of America 99(13), 8796–8801 (2002)

    Article  Google Scholar 

  15. Munroe, S.H., Lazar, M.A.: Inhibition of C-Erba Messenger-Rna Splicing by a Naturally-Occurring Antisense Rna. Journal of Biological Chemistry 266(33), 22083–22086 (1991)

    Google Scholar 

  16. Hastings, M.L., et al.: Post-transcriptional regulation of thyroid hormone receptor expression by cis-acting sequences and a naturally occurring antisense RNA. Journal of Biological Chemistry 275(15), 11507–11513 (2000)

    Article  Google Scholar 

  17. Lee, J.T., Davidow, L.S., Warshawsky, D.: Tsix, a gene antisense to Xist at the X-inactivation centre. Nature Genetics 21(4), 400–404 (1999)

    Article  Google Scholar 

  18. Bass, B.L.: RNA editing by adenosine deaminases that act on RNA. Annual Review of Biochemistry 71, 817–846 (2002)

    Article  Google Scholar 

  19. Peters, N.T., et al.: RNA editing and regulation of Drosophila 4f-rnp expression by sas-10 antisense readthrough mRNA transcripts. Rna-a Publication of the Rna Society 9(6), 698–710 (2003)

    Google Scholar 

  20. Hannon, G.J.: RNA interference. Nature 418(6894), 244–251 (2002)

    Article  Google Scholar 

  21. Aravin, A.A., et al.: Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D-melanogaster germline. Current Biology 11(13), 1017–1027 (2001)

    Article  Google Scholar 

  22. Runte, M., et al.: The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A. Human Molecular Genetics 10(23), 2687–2700 (2001)

    Article  Google Scholar 

  23. Tufarelli, C., et al.: Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nature Genetics 34(2), 157–165 (2003)

    Article  Google Scholar 

  24. Zhang, Y., et al.: NATsDB: Natural Antisense Transcripts DataBase. Nucl. Acids Res. 35(suppl. 1), D156–161 (2007)

    Google Scholar 

  25. Zhang, Y., et al.: Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Research 34(12), 3465–3475 (2006)

    Article  Google Scholar 

  26. Lavorgna, G., et al.: AntiHunter: searching BLAST output for EST antisense transcripts. Bioinformatics 20(4), 583–585 (2004)

    Article  Google Scholar 

  27. Lavorgna, G., et al.: AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts. Nucleic Acids Research 33, W665–W668 (2005)

    Google Scholar 

  28. Markham, N.R., Zuker, M.: DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Research 33, W577–W581 (2005)

    Google Scholar 

  29. Dimitrov, R.A., Zuker, M.: Prediction of hybridization and melting for double-stranded nucleic acids. Biophysical Journal 87(1), 215–226 (2004)

    Article  Google Scholar 

  30. Kurtz, S., et al.: Versatile and open software for comparing large genomes. Genome Biology 5(2) (2004)

    Google Scholar 

  31. Ensembl Genome Browser [cited 2006 12/20], Available from: http://www.ensembl.org

  32. Rosok, O., Sioud, M.: Systematic search for natural antisense transcripts in eukaryotes - (Review). International Journal of Molecular Medicine 15(2), 197–203 (2005)

    Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Computer Science, Virginia Tech, McBryde 660, Blacksburg, VA, 24060,  

    Mark J. Lawson & Liqing Zhang

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  1. Mark J. Lawson
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  2. Liqing Zhang
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Ion Măndoiu Alexander Zelikovsky

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© 2007 Springer-Verlag Berlin Heidelberg

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Lawson, M.J., Zhang, L. (2007). The Identification of Antisense Gene Pairs Through Available Software. In: Măndoiu, I., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2007. Lecture Notes in Computer Science(), vol 4463. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-72031-7_34

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  • DOI: https://doi.org/10.1007/978-3-540-72031-7_34

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-72030-0

  • Online ISBN: 978-3-540-72031-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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