Model-based Identification of Helitrons Results in a New Classification of Their Families in Arabidopsis thaliana

Sébastien Tempel 1 Jacques Nicolas 1 Abdelhak El Amrani 2 Ivan Couée 2
1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
2 ECOBIO - Ecosystèmes, biodiversité, évolution [Rennes]
Abstract : Helitrons are a class of prolific transposable elements in the Arabidopsis thaliana genome. Although 37 families were identified after the recent discovery of helitrons, no systematic classification is available, because of the high variability of helitronic sequences. Since transposition proteins are supposed to interact with helitron termini, we have formalized a model of helitron based on the characterization of termini in order to carry out an exhaustive analysis of the presence of all the possible combinations of couples of these termini. This combinatorics approach resulted in the discovery of a number of novel helitron elements corresponding to associations of termini from distinct previously-described helitron families. The matrix of occurrences of termini combinations yielded a structure that revealed clusters of helitron families. This sheds light on the history of their invasion of the Arabidopsis thaliana genome.
Keywords : Combinatorial optimization Bioinformatics Sequence analysis Genome dynamics Syntactical Modelling Transposable Elements Helitron Chimera Combinatorial optimization.
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Gene, Elsevier, 2007, 403 (1-2), 〈10.1016/j.gene.2007.06.030〉
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Sébastien Tempel, Jacques Nicolas, Abdelhak El Amrani, Ivan Couée. Model-based Identification of Helitrons Results in a New Classification of Their Families in Arabidopsis thaliana. Gene, Elsevier, 2007, 403 (1-2), 〈10.1016/j.gene.2007.06.030〉. 〈inria-00180376〉

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