ArticleNucleic acids research2021
Identification of over 200-fold more hairpin ribozymes than previously known in diverse circular RNAs.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Systematic discovery of novel ribozymes with gene silencing properties from global deep-sea RNA viromes.Frontiers in microbiology · 2026Article
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- Advancing RNA phage biology through meta-omics.Nucleic acids research · 2025Review
- A general RNA-templated RNA extension activity ofRNA (New York, N.Y.) · 2025Article
- Diversity and evolution of viroids and viroid-like agents with circular RNA genomes revealed by metatranscriptome mining.Nucleic acids research · 2025Article
- Rfam 15: RNA families database in 2025.Nucleic acids research · 2025Article
- Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections.Nucleic acids research · 2024Article
- Article
- Viroid-like colonists of human microbiomes.Cell · 2024Article
- Rfam 15: RNA families database in 2025.bioRxiv : the preprint server for biology · 2024Article
- Viroid-like colonists of human microbiomes.bioRxiv : the preprint server for biology · 2024Article
- A comparative survey of the influence of small self-cleaving ribozymes on gene expression in human cell culture.RNA biology · 2024Article
- Directed Circularization of a Short RNA.Methods in molecular biology (Clifton, N.J.) · 2024Article
- CircularSTAR3D: a stack-based RNA 3D structural alignment tool for circular matching.Nucleic acids research · 2023Article
- Hybrids of RNA viruses and viroid-like elements replicate in fungi.Nature communications · 2023Article
- Discovery of natural non-circular permutations in non-coding RNAs.Nucleic acids research · 2023Article
- Article
- ViroidDB: a database of viroids and viroid-like circular RNAs.Nucleic acids research · 2022Article
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4 authors.
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Abstract
Self-cleaving ribozymes are catalytic RNAs that cut themselves at a specific inter-nucleotide linkage. They serve as a model of RNA catalysis, and as an important tool in biotechnology. For most of the nine known structural classes of self-cleaving ribozymes, at least hundreds of examples are known, and some are present in multiple domains of life. By contrast, only four unique examples of the hairpin ribozyme class are known, despite its discovery in 1986. We bioinformatically predicted 941 unique hairpin ribozymes of a different permuted form from the four previously known hairpin ribozymes, and experimentally confirmed several diverse predictions. These results profoundly expand the number of natural hairpin ribozymes, enabling biochemical analysis based on natural sequences, and suggest that a distinct permuted form is more biologically relevant. Moreover, all novel hairpins were discovered in metatranscriptomes. They apparently reside in RNA molecules that vary both in size-from 381 to 5170 nucleotides-and in protein content. The RNA molecules likely replicate as circular single-stranded RNAs, and potentially provide a dramatic increase in diversity of such RNAs. Moreover, these organisms have eluded previous attempts to isolate RNA viruses from metatranscriptomes-suggesting a significant untapped universe of viruses or other organisms hidden within metatranscriptome sequences.
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