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Etude de la dynamique des repetitions dans les genomes eucaryotes: de leur formation a leur elimination

Abstract : From bacteria to human, interspersed or in tandem, repeated sequences can cover more than 90 % of a genomic sequence. Despite their impact on the evolution and the plasticity of eukaryotic genomes, their mechanism of propagation remains still unclear. The continuous insertion of new copies should induce the increase of genome size. What are the selection pressures involved in the genome size regulation? Do these selection strength are the same in euchromatic and heterochromatic regions? In order to highlight the repeat dynamics, I first developed computational pipelines to detect segmental duplications (SDs) and tandem repeat arrays (TRs). The SD features of the detected in the Drosophila melanogaster genome, allowed us to propose a non-allelic homologous recombination mechanism as a SD formation model. This process can be induced by repeats such as TEs. Indeed, I showed the traces of transposable elements (TEs) at their breakpoints. To understand the relationship between the repeats and the chromatin structure, we investigated the repeat evolutionary dynamics by comparing their features in heterochromatin and euchromatin domains in Arabidopsis thaliana. We constructed phylogenetic trees of repeats to estimate their divergence in euchromatin and heterochromatin. The tree topology of TE families reflects transpositions by “burst”. In order to explain, the size and divergence variations of the TE copies between these two chromatic domains, we estimated the strength of repeat elimination into these regions. Our analysis suggests that the gene selection pressure effect induces in euchromatin the repeat elimination, although, in heterochromatin, the gene paucity allows to maintain the high TE density. However, the DNA loss rate estimations suggest the same fast turnover in the both chromatin domains. To counteract the TE insertion in heterochromatin, we proposed that non-allelic homologous recombination may play a significant role. This process allows to eliminate rapidly lots of copies.
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Submitted on : Friday, May 30, 2008 - 8:27:58 AM
Last modification on : Wednesday, December 9, 2020 - 3:09:22 PM
Long-term archiving on: : Friday, May 28, 2010 - 8:43:40 PM

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  • HAL Id : tel-00283414, version 1

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Anna-Sophie Fiston-Lavier. Etude de la dynamique des repetitions dans les genomes eucaryotes: de leur formation a leur elimination. Autre [q-bio.OT]. Université Pierre et Marie Curie - Paris VI, 2008. Français. ⟨tel-00283414⟩

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