Dynamique des hélitrons dans le genome d'Arabidopsis thaliana : développement de nouvelles stratégies d'analyse des éléments transposables

Sébastien Tempel 1, 2
1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
Abstract : The transposable element Helitron is a recently discovered type of transposon present in the genome of Arabidopsis thaliana. The thesis studies three relations between helitrons and their host genome: their mode of genome's invasion, the modularity of their internal sequence interne and their impact on close genes.

Helitrons are the most widely spreaded transposable elements in this genome. However they are only partially recognized by current alignment softwares. We have produced a formal grammatical model of these elements, made of two extremities separated by a highly variable sequence of bounded size. We have built the matrix of all occurrences of models crossing all possible extremities. Combinations showed preferential associations between extremities and new chimeric families of helitrons. The detection of ORFs including helicase and RPA transposition proteins has confirmed the existence of a relation between the existence of autonomous and non-autonomous helitrons and offered some cues to understand mechanisms allowing the creation of chimeric helitrons from truncated helitronic insertions. We propose finally a new nomenclature of helitrons in Arabidopsis based on their extremities instead of their global sequence.

The observation of an helitronic sequence shows a deep reorganization of nucleic domains betweeen different copies within this family. In order to understand this organization, we have design a software, DomainOrganizer, which allows to establish the domains' composition of transposable elements . DomainOrganizer detects first domains' borders from a multiple alignment and provides the list of domains. From this list it looks for a minimal number of domains that maximizes the covering of the set of sequences, using a combinatorial optimization approach. Finally DomainOrganizer clusters and visualizes the set of sequences with respect to their domains. The analysis of domains in the familly AtREP21, a family with a high variability precluding any direct phylogenetic analysis, has allowed to decipher the nature of this variability and to trace back a possible evolutionnary scenario of this family from the identification of its domains.

We have also studied the localization of helitrons in the genomic sequence of Arabidopsis thaliana and shown a preferential insertion of them in genes' promoters. Our work focused on family AtREP3 and on helitrons present at less than 1 kb from a START codon. The expression profiles of these genes reveals the existence of several clusters of similar profiles at the level of tissues. The patterns of transcription factor sites are highly variables in promoters except for helitron-containing promoters. This is in accordance with the hypothesis that non-autonomous helitrons carry patterns coding for transcription factor sites. Additional experiments have to be designed in order to fully understand the regulation of genes close to helitrons.
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Sébastien Tempel. Dynamique des hélitrons dans le genome d'Arabidopsis thaliana : développement de nouvelles stratégies d'analyse des éléments transposables. Biochimie [q-bio.BM]. Université Rennes 1, 2007. Français. ⟨tel-00185256⟩

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