Model-based identification of Helitrons results in a new classification of their families in Arabidopsis thaliana

• Published in: Gene Vol. 403; no. 1; pp. 18 - 28
• Main Authors: Tempel, Sébastien, Nicolas, Jacques, El Amrani, Abdelhak, Couée, Ivan
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 15.11.2007; Elsevier
• Subjects: Arabidopsis - classification; Arabidopsis - genetics; Arabidopsis thaliana; Base Sequence; Bioinformatics; Chimera; Chromosomes, Plant; Cluster Analysis; Combinatorial optimization; Computational Biology - methods; Computer Science; DNA Transposable Elements - genetics; DNA, Plant - chemistry; DNA, Plant - genetics; Genome dynamics; Genome, Plant; Life Sciences; Models, Genetic; Molecular Sequence Data; Plant Proteins - genetics; Plant Proteins - metabolism; Quantitative Methods; Sequence analysis; Sequence Analysis, DNA; Syntactical modeling; Terminology as Topic; Transposable elements; ss; Genome dynamics; RPA; STAN; Combinatorial optimization; Bioinformatics; Sequence analysis; Syntactical modeling; Transposable elements; Chimera; Syntactical Modelling; Helitron; Transposable Elements
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2007.06.030

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 assumed to interact with Helitron termini, a Helitron model was formalized based on terminus characterization in order to carry out an exhaustive analysis of all possible combinations of the pairs of termini present. This combinatorics approach resulted in the discovery of a number of new Helitron elements corresponding to termini associations from distinct previously-described Helitron families. The occurrence matrix of termini combinations yielded a structure that revealed clusters of Helitron families.