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R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements

BACKGROUND: R2 is a non-long terminal repeat (non-LTR) retrotransposable element that inserts site specifically into the 28S genes of the ribosomal (r)RNA gene loci. Encoded at the 5' end is a ribozyme that generates the precise 5' end by self-cleavage of a 28S gene cotranscript. Sequences...

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Autores principales: Eickbush, Danna G, Eickbush, Thomas H
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3414825/
https://www.ncbi.nlm.nih.gov/pubmed/22621441
http://dx.doi.org/10.1186/1759-8753-3-10
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author Eickbush, Danna G
Eickbush, Thomas H
author_facet Eickbush, Danna G
Eickbush, Thomas H
author_sort Eickbush, Danna G
collection PubMed
description BACKGROUND: R2 is a non-long terminal repeat (non-LTR) retrotransposable element that inserts site specifically into the 28S genes of the ribosomal (r)RNA gene loci. Encoded at the 5' end is a ribozyme that generates the precise 5' end by self-cleavage of a 28S gene cotranscript. Sequences at the 3' end are necessary for the R2 protein to bind RNA and initiate the target primed reverse transcription (TPRT) reaction. These minimal RNA requirements suggested that if recombination/DNA repair conjoined the 5' and 3' ends of R2, the result would be a non-autonomous element that could survive as long as autonomous R2 elements supplied the TPRT activity. RESULTS: A PCR-based survey of 39 Drosophila species aided by genomic sequences from 12 of these species revealed two types of non-autonomous elements. We call these elements SIDEs (for ‘Short Internally Deleted Elements’). The first consisted of a 5' ribozyme and a 3' end of an R2 element as predicted. Variation at the 5' junctions of the R2 SIDE copies was typical for R2 insertions suggesting their propagation by TPRT. The second class of SIDE contained sequences from R1 elements, another non-LTR retrotransposon that inserts into rRNA gene loci. These insertions had an R2 ribozyme immediately upstream of R1 3' end sequences. These hybrid SIDEs were inserted at the R1 site with 14 bp target site duplications typical of R1 insertions suggesting they used the R1 machinery for retrotransposition. Finally, the survey revealed examples of U12 small nuclear (sn)RNA and tRNA sequences at the 5' end of R2 elements suggesting the R2 reverse transcriptase can template jump from the R2 transcript to a second RNA during TPRT. CONCLUSIONS: The R2 SIDE and R2/R1 hybrid SIDEs are rare examples of non-autonomous retrotransposons in the Drosophila genome. Associated non-autonomous elements and in vivo template jumps are two additional characteristics R2 shares with other non-LTR retrotransposons such as mammalian L1s. Analysis of the hybrid SIDEs provides supporting evidence that R1 elements, like R2 elements, recognize their 3' untranslated region (UTR) sequences and, thus, belong to the stringent class of non-LTR elements.
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spelling pubmed-34148252012-08-10 R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements Eickbush, Danna G Eickbush, Thomas H Mob DNA Research BACKGROUND: R2 is a non-long terminal repeat (non-LTR) retrotransposable element that inserts site specifically into the 28S genes of the ribosomal (r)RNA gene loci. Encoded at the 5' end is a ribozyme that generates the precise 5' end by self-cleavage of a 28S gene cotranscript. Sequences at the 3' end are necessary for the R2 protein to bind RNA and initiate the target primed reverse transcription (TPRT) reaction. These minimal RNA requirements suggested that if recombination/DNA repair conjoined the 5' and 3' ends of R2, the result would be a non-autonomous element that could survive as long as autonomous R2 elements supplied the TPRT activity. RESULTS: A PCR-based survey of 39 Drosophila species aided by genomic sequences from 12 of these species revealed two types of non-autonomous elements. We call these elements SIDEs (for ‘Short Internally Deleted Elements’). The first consisted of a 5' ribozyme and a 3' end of an R2 element as predicted. Variation at the 5' junctions of the R2 SIDE copies was typical for R2 insertions suggesting their propagation by TPRT. The second class of SIDE contained sequences from R1 elements, another non-LTR retrotransposon that inserts into rRNA gene loci. These insertions had an R2 ribozyme immediately upstream of R1 3' end sequences. These hybrid SIDEs were inserted at the R1 site with 14 bp target site duplications typical of R1 insertions suggesting they used the R1 machinery for retrotransposition. Finally, the survey revealed examples of U12 small nuclear (sn)RNA and tRNA sequences at the 5' end of R2 elements suggesting the R2 reverse transcriptase can template jump from the R2 transcript to a second RNA during TPRT. CONCLUSIONS: The R2 SIDE and R2/R1 hybrid SIDEs are rare examples of non-autonomous retrotransposons in the Drosophila genome. Associated non-autonomous elements and in vivo template jumps are two additional characteristics R2 shares with other non-LTR retrotransposons such as mammalian L1s. Analysis of the hybrid SIDEs provides supporting evidence that R1 elements, like R2 elements, recognize their 3' untranslated region (UTR) sequences and, thus, belong to the stringent class of non-LTR elements. BioMed Central 2012-05-23 /pmc/articles/PMC3414825/ /pubmed/22621441 http://dx.doi.org/10.1186/1759-8753-3-10 Text en Copyright ©2012 Eickbush and Eickbush; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Eickbush, Danna G
Eickbush, Thomas H
R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements
title R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements
title_full R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements
title_fullStr R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements
title_full_unstemmed R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements
title_short R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements
title_sort r2 and r2/r1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3414825/
https://www.ncbi.nlm.nih.gov/pubmed/22621441
http://dx.doi.org/10.1186/1759-8753-3-10
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