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International Symposium on Bioinformatics Research and Applications

ISBRA 2012: Bioinformatics Research and Applications pp 48–59Cite as

A Transcript Perspective on Evolution

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 7292))

Abstract

Alternative splicing is now recognized as a major mechanism for transcriptome and proteome diversity in higher eukaryotes. Yet, its evolution is poorly understood. Most studies focus on the evolution of exons and introns at the gene level, while only few consider the evolution of transcripts.

In this paper, we present a framework for transcript phylogenies where ancestral transcripts evolve along the gene tree by gains, losses, and mutation. We demonstrate the usefulness of our method on a set of 805 genes and two different topics. First, we improve a method for transcriptome reconstruction from ESTs (ASPic), then we study the evolution of function in transcripts. The use of transcript phylogenies allows us to double the specificity of ASPic, whereas results on the functional study reveal that conserved transcripts are more likely to share protein domains than functional sites. These studies validate our framework for the study of evolution in large collections of organisms from the perspective of transcripts; we developed and provide a new tool, TrEvoR, for this purpose.

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References

  1. Kim, N., Shin, S., Lee, S.: ECgene: genome-based EST clustering and gene modeling for alternative splicing. Genome Research 15(4), 566–576 (2005)

    Article  MathSciNet  Google Scholar 

  2. Modrek, B., Lee, C.: A genomic view of alternative splicing. Nature Genetics 30(1), 13–19 (2002)

    Article  Google Scholar 

  3. Keren, H., Lev-Maor, G., Ast, G.: Alternative splicing and evolution: diversification, exon definition and function. Nature Reviews Genetics 11(5), 345–355 (2010)

    Article  Google Scholar 

  4. Artamonova, I.I., Gelfand, M.S.: Comparative genomics and evolution of alternative splicing: the pessimists’ science. Chemical Reviews 107(8), 3407–3430 (2007)

    Article  Google Scholar 

  5. Harr, B., Turner, L.M.: Genome-wide analysis of alternative splicing evolution among Mus subspecies. Molecular Ecology 19(suppl.1), 228–239 (2010)

    Article  Google Scholar 

  6. Nurtdinov, R.N.: Low conservation of alternative splicing patterns in the human and mouse genomes. Human Molecular Genetics 12(11), 1313–1320 (2003)

    Article  Google Scholar 

  7. Flicek, P., et al.: Ensembl 10th year. Nucleic Acids Research 38(suppl.1), D557–D562 (2010)

    Article  Google Scholar 

  8. Christinat, Y., Moret, B.: Inferring transcript phylogenies. In: Proc. of IEEE International Conference on Bioinformatics and Biomedecine, pp. 208–215 (2011)

    Google Scholar 

  9. Martelli, P., et al.: ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Research 39(suppl.1), D80 (2011)

    Article  MathSciNet  Google Scholar 

  10. Pruitt, K., et al.: NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Research 37(suppl.1), D32–D36 (2009)

    Article  Google Scholar 

  11. Bonizzoni, P., et al.: Detecting alternative gene structures from spliced ESTs: a computational approach. Journal of Computational Biology 16(1), 43–66 (2009)

    Article  MathSciNet  Google Scholar 

  12. Eyras, E., et al.: ESTGenes: alternative splicing from ESTs in Ensembl. Genome Research 14(5), 976–987 (2004)

    Article  Google Scholar 

  13. Guttman, M., et al.: Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincrnas. Nature Biotechnology 28(5), 503–510 (2010)

    Article  Google Scholar 

  14. Trapnell, C., et al.: Transcript assembly and quantification by rna-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 28(5), 511–515 (2010)

    Article  Google Scholar 

  15. Xing, Y., et al.: An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Research 34(10), 3150 (2006)

    Article  Google Scholar 

  16. Cline, M., et al.: The effects of alternative splicing on transmembrane proteins in the mouse genome. In: Pac. Symp. Biocomput. 2004, pp. 17–28 (2004)

    Google Scholar 

  17. Eden, E., et al.: GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10(1), 48 (2009)

    Article  MathSciNet  Google Scholar 

  18. Sankoff, D.: Minimal Mutation Trees of Sequences. SIAM Journal on Applied Mathematics 28(1), 35–42 (1975)

    Article  MathSciNet  MATH  Google Scholar 

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Author information

Authors and Affiliations

  1. Laboratory of Computational Biology and Bioinformatics, EPFL, 1015, Lausanne, Switzerland

    Yann Christinat & Bernard M. E. Moret

Authors
  1. Yann Christinat
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  2. Bernard M. E. Moret
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Editor information

Editors and Affiliations

  1. Departments of Bioengineering and Electrical Engineering, University of Texas at Dallas, 75080, Richardson, TX, USA

    Leonidas Bleris

  2. Department of Computer Science and Engineering, University of Connecticut, 06269, Storrs, CT, USA

    Ion Măndoiu

  3. Department of Biological Sciences, Carnegie Mellon University, 15213, Pittsburgh, PA, USA

    Russell Schwartz

  4. School of Information Science and Engineering, Central South University, 410083, Changsha, China

    Jianxin Wang

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© 2012 Springer-Verlag Berlin Heidelberg

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Christinat, Y., Moret, B.M.E. (2012). A Transcript Perspective on Evolution. In: Bleris, L., Măndoiu, I., Schwartz, R., Wang, J. (eds) Bioinformatics Research and Applications. ISBRA 2012. Lecture Notes in Computer Science(), vol 7292. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30191-9_5

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  • DOI: https://doi.org/10.1007/978-3-642-30191-9_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-30190-2

  • Online ISBN: 978-3-642-30191-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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