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MBE Advance Access originally published online on November 2, 2005
Molecular Biology and Evolution 2006 23(2):411-420; doi:10.1093/molbev/msj046
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

The Trypanosoma cruzi L1Tc and NARTc Non-LTR Retrotransposons Show Relative Site Specificity for Insertion

Frédéric Bringaud*, Daniella C. Bartholomeu{dagger}, Gaëlle Blandin{dagger}, Arthur Delcher{dagger}, Théo Baltz*, Najib M. A. El-Sayed{dagger},{ddagger} and Elodie Ghedin{dagger},{ddagger}

* Laboratoire de Génomique Fonctionnelle des Trypanosomatides, UMR-5162 Centre National de la Recherche Scientifique, Université Victor Segalen Bordeaux 2, Bordeaux Cedex, France; {dagger} The Institute for Genomic Research, Rockville; and {ddagger} Department of Microbiology and Tropical Medicine, George Washington University

E-mail: bringaud{at}u-bordeaux2.fr.

The trypanosomatid protozoan Trypanosoma cruzi contains long autonomous (L1Tc) and short nonautonomous (NARTc) non–long terminal repeat retrotransposons. NARTc (0.25 kb) probably derived from L1Tc (4.9 kb) by 3'-deletion. It has been proposed that their apparent random distribution in the genome is related to the L1Tc-encoded apurinic/apyrimidinic endonuclease (APE) activity, which repairs modified residues. To address this question we used the T. cruzi (CL-Brener strain) genome data to analyze the distribution of all the L1Tc/NARTc elements present in contigs larger than 10 kb. This data set, which represents 0.91x sequence coverage of the haploid nuclear genome (~55 Mb), contains 419 elements, including 112 full-length L1Tc elements (14 of which are potentially functional) and 84 full-length NARTc. Approximately half of the full-length elements are flanked by a target site duplication, most of them (87%) are 12 bp long. Statistical analyses of sequences flanking the full-length elements show the same highly conserved pattern upstream of both the L1Tc and NARTc retrotransposons. The two most conserved residues are a guanine and an adenine, which flank the site where first-strand cleavage is performed by the element-encoded endonuclease activity. This analysis clearly indicates that the L1Tc and NARTc elements display relative site specificity for insertion, which suggests that the APE activity is not responsible for first-strand cleavage of the target site.

Key Words: apurinic/apyrimidinic endonuclease • L1Tc • NARTc • non-LTR retrotransposon • retroposon • site specificity • Trypanosoma cruzi


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