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Cited by 81Chromosomal and Genetic VariationsGenomics and Chromatin DynamicsEvolution and Genetic Dynamics

Integration, regulation, and long-term stability of R2 retrotransposons

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Eickbush, Thomas H., Eickbush, Danna G.·2015·Microbiology Spectrum
DOI 10.1128/microbiolspec.mdna3-0011-2014PMC PMC4498411
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Abstract

R2 elements are sequence specific non-LTR retrotransposons that exclusively insert in the 28S rRNA genes of animals. R2s encode an endonuclease that cleaves the insertion site and a reverse transcriptase that uses the cleaved DNA to prime reverse transcription of the R2 transcript, a process termed target primed reverse transcription. Additional unusual properties of the reverse transcriptase as well as DNA and RNA binding domains of the R2 encoded protein have been characterized. R2 expression is through co-transcription with the 28S gene and self-cleavage by a ribozyme encoded at the R2 5′ end. Studies in laboratory stocks and natural populations of Drosophila suggest that R2 expression is tied to the distribution of R2-inserted units within the rDNA locus. Most individuals have no R2 expression because only a small fraction of their rRNA genes need to be active, and a contiguous region of the locus free of R2 insertions can be selected for activation. However, if the R2-free region is not large enough to produce sufficient rRNA, flanking units - including those inserted with R2 - must be activated. Finally, R2 copies rapidly turnover within the rDNA locus, yet R2 has been vertically maintained in animal lineages for hundreds of millions of years. The key to this stability is R2's ability to remain dormant in rDNA units outside the transcribed regions for generations until the stochastic nature of the crossovers that drive the concerted evolution of the rDNA locus inevitably reshuffle the inserted and uninserted units, resulting in transcription of the R2-inserted units.

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  • Some rDNA units contain R1/R2 insertions shortened to varying degrees from the 5′-end, formed due to abortive reverse transcription.

    “Some rDNA units contain R1/R2 insertions shortened to varying degrees from the 5′-end, formed due to abortive reverse transcription (30,41).”

    From Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon (2022) · cites this paper as [30]

    The section “R2 copies are rapidly gained and lost from rDNA loci” describes R2 insertions with 5′ truncations of varying lengths. “Current model of R2 integration” says these arise when reverse transcriptase does not reach the 5′ end of the RNA template. The Introduction places R1 insertions in rDNA, but our copy does not establish the same truncation mechanism for R1. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • Full-length R2 insertions encode a ribozyme that releases the 5′-end of the R2 transcript from the upstream 28S rRNA sequence during the autocatalytic reaction.

    “Full-length R2 insertions encode a ribozyme, which releases the 5′-end of the R2 transcript from the upstream 28S rRNA sequence during the autocatalytic reaction (Figure 1A)”

    From Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon (2022) · cites this paper as [30]

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Authors
Eickbush, T. H., & Eickbush, D. G.
Affiliations
University of Rochester (US)
Venue
Microbiology Spectrum
Publisher
American Society for Microbiology
Published
2015-04-02
Volume
3
Issue
2
Pages
MDNA3-0011
ISSN
2165-0497 (ISSN-L)
DOI
10.1128/microbiolspec.mdna3-0011-2014
PMC
PMC4498411
OpenAlex
W858000480
Cited by
81
References
8
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FWCI
0.31
Type
journal article
Language
en
Open access
Licence
journals.asm.org/non-commercial-tdm-license (tdm)
Locations
  • Microbiology Spectrum (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
National Institute of General Medical Sciences (R01GM42790, R01GM042790)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords
R2 retrotransposon, non-LTR retrotransposons, 28S rRNA gene, rDNA locus, target-primed reverse transcription, Drosophila, transposable element regulation, concerted evolution, transposon insertion
MeSH terms
Animals, Binding Sites, DNA, Ribosomal, Gene Expression Regulation, Recombination, Genetic, RNA-Directed DNA Polymerase, RNA, Ribosomal, 28S, Mutagenesis, Insertional, Short Interspersed Nucleotide Elements, Genomic Instability, Reverse Transcription

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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