ArticlePloS one2013
Evolution of the R2 retrotransposon ribozyme and its self-cleavage site.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 25 citations in OpenAlex.
- Discovery and engineering of avian R2 retrotransposons for all-RNA-mediated targeted DNA integration in human cells.Nature biotechnology · 2026Article
- Diversity and genome engineering applications of R2 non-LTR retrotransposons.RNA (New York, N.Y.) · 2026Review
- DNA-bound avian R2 non-LTR retrotransposon protein recruits a second R2 protein for genome-protective second-strand nicking.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Optimized R2 retroelement complexes for DNA insertion into plant genomes.Nature biotechnology · 2026Article
- Single-turnover kinetic analysis of non-long terminal repeat retrotransposition defines the pathway and rate constants leading to second-strand synthesis.Nucleic acids research · 2026Article
- Rewriting the genome: harnessing R2 retrotransposons for precise DNA insertion.Frontiers in genome editing · 2026Review
- Structure and biochemistry-guided engineering of an all-RNA system for DNA insertion with R2 retrotransposons.Nature communications · 2025Article
- Article
- Harnessing eukaryotic retroelement proteins for transgene insertion into human safe-harbor loci.Nature biotechnology · 2025Article
- Structure and sequence at an RNA template 5' end influence insertion of transgenes by an R2 retrotransposon protein.RNA (New York, N.Y.) · 2024Article
- Distinct and overlapping RNA determinants for binding and target-primed reverse transcription by Bombyx mori R2 retrotransposon protein.Nucleic acids research · 2024Article
- The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics.Molecular biology and evolution · 2024Article
- Experimental considerations for precise RNA-mediated insertion of transgenes.Methods in enzymology · 2024Article
- Structure of the R2 non-LTR retrotransposon initiating target-primed reverse transcription.Science (New York, N.Y.) · 2023Article
- Article
- Sequence-specific retrotransposition of 28S rDNA-specific LINE R2Ol in human cells.RNA (New York, N.Y.) · 2019Article
- Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function.Nucleic acids research · 2019Article
- Completion of LINE integration involves an open '4-way' branched DNA intermediate.Nucleic acids research · 2019Article
- Convergent evolution of ribonuclease h in LTR retrotransposons and retroviruses.Molecular biology and evolution · 2015Article
- Integration, Regulation, and Long-Term Stability of R2 Retrotransposons.Microbiology spectrum · 2015Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
R2 is a non-long terminal repeat retrotransposon that inserts site-specifically in the tandem 28S rRNA genes of many animals. Previously, R2 RNA from various species of Drosophila was shown to self-cleave from the 28S rRNA/R2 co-transcript by a hepatitis D virus (HDV)-like ribozyme encoded at its 5' end. RNA cleavage was at the precise 5' junction of the element with the 28S gene. Here we report that RNAs encompassing the 5' ends of R2 elements from throughout its species range fold into HDV-like ribozymes. In vitro assays of RNA self-cleavage conducted in many R2 lineages confirmed activity. For many R2s, RNA self-cleavage was not at the 5' end of the element but at 28S rRNA sequences up to 36 nucleotides upstream of the junction. The location of cleavage correlated well with the types of endogenous R2 5' junctions from different species. R2 5' junctions were uniform for most R2s in which RNA cleavage was upstream in the rRNA sequences. The 28S sequences remaining on the first DNA strand synthesized during retrotransposition are postulated to anneal to the target site and uniformly prime second strand DNA synthesis. In species where RNA cleavage occurred at the R2 5' end, the 5' junctions were variable. This junction variation is postulated to result from the priming of second strand DNA synthesis by chance microhomologies between the target site and the first DNA strand. Finally, features of R2 ribozyme evolution, especially changes in cleavage site and convergence on the same active site sequences, are discussed.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.