ArticleMolecular biology and evolution2014
Eukaryotic penelope-like retroelements encode hammerhead ribozyme motifs.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed, 59 citations in OpenAlex.
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- An Ancient Clade of Penelope-Like Retroelements with Permuted Domains Is Present in the Green Lineage and Protists, and Dominates Many Invertebrate Genomes.Molecular biology and evolution · 2021Article
- Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni.Genome biology and evolution · 2021Article
- Hepatitis delta virus-like circular RNAs from diverse metazoans encode conserved hammerhead ribozymes.Virus evolution · 2021Article
- A Singular and Widespread Group of Mobile Genetic Elements: RNA Circles with Autocatalytic Ribozymes.Cells · 2020Review
- Small circRNAs with self-cleaving ribozymes are highly expressed in diverse metazoan transcriptomes.Nucleic acids research · 2020Article
- Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function.Nucleic acids research · 2019Article
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- MGERT: a pipeline to retrieve coding sequences of mobile genetic elements from genome assemblies.Mobile DNA · 2019Article
- Viroid research and its significance for RNA technology and basic biochemistry.Nucleic acids research · 2018Review
- Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers.RNA biology · 2017Article
- Giant Reverse Transcriptase-Encoding Transposable Elements at Telomeres.Molecular biology and evolution · 2017Article
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2 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Small self-cleaving RNAs, such as the paradigmatic Hammerhead ribozyme (HHR), have been recently found widespread in DNA genomes across all kingdoms of life. In this work, we found that new HHR variants are preserved in the ancient family of Penelope-like elements (PLEs), a group of eukaryotic retrotransposons regarded as exceptional for encoding telomerase-like retrotranscriptases and spliceosomal introns. Our bioinformatic analysis revealed not only the presence of minimalist HHRs in the two flanking repeats of PLEs but also their massive and widespread occurrence in metazoan genomes. The architecture of these ribozymes indicates that they may work as dimers, although their low self-cleavage activity in vitro suggests the requirement of other factors in vivo. In plants, however, PLEs show canonical HHRs, whereas fungi and protist PLEs encode ribozyme variants with a stable active conformation as monomers. Overall, our data confirm the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eukaryotic genomes.
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