Genomic signatures: tracing the origin of retroelements at the nucleotide level |
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Authors: | Christophe Terzian Ivan Laprevotte Sophie Brouillet Alain Hénaut |
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Institution: | (1) Centre de Génétique Moléculaire, CNRS, 91198 Gif-sur-Yvette, cedex, France |
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Abstract: | We investigate the nucleotide sequences of 23 retroelements (4 mammalian retroviruses, 1 human, 3 yeast, 2 plant, and 13 invertebrate
retrotransposons) in terms of their oligonucleotide composition in order to address the problem of relationship between retrotransposons
and retroviruses, and the coadaptation of these retroelements to their host genomes. We have identified by computer analysis
over-represented 3- through 6-mers in each sequence. Our results indicate retrotransposons are heterogeneous in contrast to
retroviruses, suggesting different modes of evolution by slippage-like mechanisms. Moreover, we have calculated the Observed/Expected
number ratio for each of the 256 tetramers and analysed the data using a multivariate approach. The tetramer composition of
retroelement sequences appears to be influenced by host genomic factors like methylase activity.
This revised version was published online in August 2006 with corrections to the Cover Date. |
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Keywords: | retrotransposons retroviruses oligonucleotide composition multivariate analysis |
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