title: The Trypanosoma cruzi L1Tc and NARTc non-LTR retrotransposons show relative site specificity for insertion.
abstract: 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 ( approximately 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.
authors.affiliation: Laboratoire de Génomique Fonctionnelle des Trypanosomatides, UMR-5162 Centre National de la Recherche Scientifique, Université Victor Segalen Bordeaux 2, Bordeaux Cedex, France. bringaud@u-bordeaux2.fr
authors.forename: Frédéric
authors.initials: F
authors.lastname: Bringaud
authors.forename: Daniella C
authors.initials: DC
authors.lastname: Bartholomeu
authors.forename: Gaëlle
authors.initials: G
authors.lastname: Blandin
authors.forename: Arthur
authors.initials: A
authors.lastname: Delcher
authors.forename: Théo
authors.initials: T
authors.lastname: Baltz
authors.forename: Najib M A
authors.initials: NM
authors.lastname: El-Sayed
authors.forename: Elodie
authors.initials: E
authors.lastname: Ghedin
mesh_terms: D000818:Animals; D016054:DNA, Protozoan / Q000235:genetics* / Q000378:metabolism; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase / Q000235:genetics / Q000378:metabolism; D016254:Mutagenesis, Insertional; D018626:Retroelements / Q000235:genetics*; D017384:Sequence Deletion; D014349:Trypanosoma cruzi / Q000235:genetics* / Q000378:metabolism
chemical_list: D016054:DNA, Protozoan; D018626:Retroelements; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase