Model-based identification of Helitrons results in a new classification of their families in Arabidopsis thaliana.
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.
Tempel
Sébastien
S
IRISA-INRIA, Campus de Beaulieu Bâtiment 12, 35042 Rennes cedex, France.
Nicolas
Jacques
J
El Amrani
Abdelhak
A
Couée
Ivan
I
D017360:Arabidopsis / Q000145:classification* / Q000235:genetics*; D001483:Base Sequence; D032461:Chromosomes, Plant; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D004251:DNA Transposable Elements / Q000235:genetics*; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D018745:Genome, Plant; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D009626:Terminology as Topic
D004251:DNA Transposable Elements; D018744:DNA, Plant; D010940:Plant Proteins