The ingi and RIME non-LTR Retrotransposons are Not Randomly Distributed in the Genome of Trypanosoma brucei

Frédéric Bringaud, Nicolas Biteau, Eduard Zuiderwijk, Matthew Berriman, Najib M. El-Sayed, Elodie Ghedin, Sara E. Melville, Neil Hall, Théo Baltz

Research output: Contribution to journalArticle

Abstract

The ingi (long and autonomous) and RIME (short and nonautonomous) non-long-terminal repeat retrotransposons are the most abundant mobile elements characterized to date in the genome of the African trypanosome Trypanosoma brucei. These retrotransposons were thought to be randomly distributed, but a detailed and comprehensive analysis of their genomic distribution had not been performed until now. To address this question, we analyzed the ingi/RIME sequences and flanking sequences from the ongoing T. brucei genome sequencing project (TREU927/4 strain). Among the 81 ingi/ RIME elements analyzed, 60% are complete, and 7% of the ingi elements (approximately 15 copies per haploid genome) appear to encode for their own transposition. The size of the direct repeat flanking the ingi/RIME retrotransposons is conserved (i.e., 12-bp), and a strong 11-bp consensus pattern precedes the 5′-direct repeat. The presence of a consensus pattern upstream of the retroelements was confirmed by the analysis of the base occurrence in 294 GSS containing 5′-adjacent ingi/RIME sequences. The conserved sequence is present upstream of ingis and RIMEs, suggesting that ingi-encoded enzymatic activities are used for retrotransposition of RIMEs, which are short nonautonomous retroelements. In conclusion, the ingi and RIME retroelements are not randomly distributed in the genome of T. brucei and are preceded by a conserved sequence, which may be the recognition site of the ingi-encoded endonuclease.

Original languageEnglish (US)
Pages (from-to)520-528
Number of pages9
JournalMolecular Biology and Evolution
Volume21
Issue number3
DOIs
StatePublished - Mar 2004

Fingerprint

Trypanosoma brucei
Retroelements
Trypanosoma brucei brucei
retrotransposons
genome
Genes
Genome
conserved sequences
Conserved Sequence
Nucleic Acid Repetitive Sequences
genomics
terminal repeat sequences
Trypanosomiasis
Terminal Repeat Sequences
transposition (genetics)
Endonucleases
Haploidy
haploidy
analysis

Keywords

  • ingi
  • Insertion site specificity
  • Non-LTR retrotransposon
  • Retroelement hot spot gene
  • RIME
  • Trypanosoma brucei

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 ingi and RIME non-LTR Retrotransposons are Not Randomly Distributed in the Genome of Trypanosoma brucei. / Bringaud, Frédéric; Biteau, Nicolas; Zuiderwijk, Eduard; Berriman, Matthew; El-Sayed, Najib M.; Ghedin, Elodie; Melville, Sara E.; Hall, Neil; Baltz, Théo.

In: Molecular Biology and Evolution, Vol. 21, No. 3, 03.2004, p. 520-528.

Research output: Contribution to journalArticle

Bringaud, F, Biteau, N, Zuiderwijk, E, Berriman, M, El-Sayed, NM, Ghedin, E, Melville, SE, Hall, N & Baltz, T 2004, 'The ingi and RIME non-LTR Retrotransposons are Not Randomly Distributed in the Genome of Trypanosoma brucei', Molecular Biology and Evolution, vol. 21, no. 3, pp. 520-528. https://doi.org/10.1093/molbev/msh045
Bringaud, Frédéric ; Biteau, Nicolas ; Zuiderwijk, Eduard ; Berriman, Matthew ; El-Sayed, Najib M. ; Ghedin, Elodie ; Melville, Sara E. ; Hall, Neil ; Baltz, Théo. / The ingi and RIME non-LTR Retrotransposons are Not Randomly Distributed in the Genome of Trypanosoma brucei. In: Molecular Biology and Evolution. 2004 ; Vol. 21, No. 3. pp. 520-528.
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abstract = "The ingi (long and autonomous) and RIME (short and nonautonomous) non-long-terminal repeat retrotransposons are the most abundant mobile elements characterized to date in the genome of the African trypanosome Trypanosoma brucei. These retrotransposons were thought to be randomly distributed, but a detailed and comprehensive analysis of their genomic distribution had not been performed until now. To address this question, we analyzed the ingi/RIME sequences and flanking sequences from the ongoing T. brucei genome sequencing project (TREU927/4 strain). Among the 81 ingi/ RIME elements analyzed, 60{\%} are complete, and 7{\%} of the ingi elements (approximately 15 copies per haploid genome) appear to encode for their own transposition. The size of the direct repeat flanking the ingi/RIME retrotransposons is conserved (i.e., 12-bp), and a strong 11-bp consensus pattern precedes the 5′-direct repeat. The presence of a consensus pattern upstream of the retroelements was confirmed by the analysis of the base occurrence in 294 GSS containing 5′-adjacent ingi/RIME sequences. The conserved sequence is present upstream of ingis and RIMEs, suggesting that ingi-encoded enzymatic activities are used for retrotransposition of RIMEs, which are short nonautonomous retroelements. In conclusion, the ingi and RIME retroelements are not randomly distributed in the genome of T. brucei and are preceded by a conserved sequence, which may be the recognition site of the ingi-encoded endonuclease.",
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AU - Berriman, Matthew

AU - El-Sayed, Najib M.

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AU - Melville, Sara E.

AU - Hall, Neil

AU - Baltz, Théo

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N2 - The ingi (long and autonomous) and RIME (short and nonautonomous) non-long-terminal repeat retrotransposons are the most abundant mobile elements characterized to date in the genome of the African trypanosome Trypanosoma brucei. These retrotransposons were thought to be randomly distributed, but a detailed and comprehensive analysis of their genomic distribution had not been performed until now. To address this question, we analyzed the ingi/RIME sequences and flanking sequences from the ongoing T. brucei genome sequencing project (TREU927/4 strain). Among the 81 ingi/ RIME elements analyzed, 60% are complete, and 7% of the ingi elements (approximately 15 copies per haploid genome) appear to encode for their own transposition. The size of the direct repeat flanking the ingi/RIME retrotransposons is conserved (i.e., 12-bp), and a strong 11-bp consensus pattern precedes the 5′-direct repeat. The presence of a consensus pattern upstream of the retroelements was confirmed by the analysis of the base occurrence in 294 GSS containing 5′-adjacent ingi/RIME sequences. The conserved sequence is present upstream of ingis and RIMEs, suggesting that ingi-encoded enzymatic activities are used for retrotransposition of RIMEs, which are short nonautonomous retroelements. In conclusion, the ingi and RIME retroelements are not randomly distributed in the genome of T. brucei and are preceded by a conserved sequence, which may be the recognition site of the ingi-encoded endonuclease.

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