The Trypanosoma cruzi L1Tc and NARTc non-LTR retrotransposons show relative site specificity for insertion

Frédéric Bringaud, Daniella C. Bartholomeu, Gaëlle Blandin, Arthur Delcher, Théo Baltz, Najib M A El-Sayed, Elodie Ghedin

Research output: Contribution to journalArticle

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 0.91 X 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.

Original languageEnglish (US)
Pages (from-to)411-420
Number of pages10
JournalMolecular Biology and Evolution
Volume23
Issue number2
DOIs
StatePublished - Feb 2006

Fingerprint

Retroelements
Trypanosoma cruzi
Endonucleases
retrotransposons
genome
Genes
Genome
cleavage
DNA-(Apurinic or Apyrimidinic Site) Lyase
Terminal Repeat Sequences
Haploidy
Guanine
Adenine
Trypanosomatidae
repair
terminal repeat sequences
Sequence Analysis
guanine
Repair
adenine

Keywords

  • Apurinic/apyrimidinic endonuclease
  • L1Tc
  • NARTc
  • Non-LTR retrotransposon
  • Retroposon
  • Site specificity
  • Trypanosoma cruzi

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Genetics(clinical)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Ecology, Evolution, Behavior and Systematics
  • Agricultural and Biological Sciences (miscellaneous)
  • Molecular Biology

Cite this

The Trypanosoma cruzi L1Tc and NARTc non-LTR retrotransposons show relative site specificity for insertion. / Bringaud, Frédéric; Bartholomeu, Daniella C.; Blandin, Gaëlle; Delcher, Arthur; Baltz, Théo; El-Sayed, Najib M A; Ghedin, Elodie.

In: Molecular Biology and Evolution, Vol. 23, No. 2, 02.2006, p. 411-420.

Research output: Contribution to journalArticle

Bringaud, Frédéric ; Bartholomeu, Daniella C. ; Blandin, Gaëlle ; Delcher, Arthur ; Baltz, Théo ; El-Sayed, Najib M A ; Ghedin, Elodie. / The Trypanosoma cruzi L1Tc and NARTc non-LTR retrotransposons show relative site specificity for insertion. In: Molecular Biology and Evolution. 2006 ; Vol. 23, No. 2. pp. 411-420.
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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 0.91 X 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.",
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AU - Blandin, Gaëlle

AU - Delcher, Arthur

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