ArticleThe Journal of biological chemistry2011
Structure-based search reveals hammerhead ribozymes in the human microbiome.
Article in The Journal of biological chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Rapid discovery of functional RNA domains.Nucleic acids research · 2025Article
- Article
- Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes.Genomics, proteomics & bioinformatics · 2024Article
- The structure and catalytic mechanism of a pseudoknot-containing hammerhead ribozyme.Nature communications · 2024Article
- Genome-Wide Computational Prediction and Analysis of Noncoding RNAs inMicroorganisms · 2024Article
- Identification of Hammerhead-variant ribozyme sequences in SARS-CoV-2.Nucleic acids research · 2024Article
- Computational design and experimental verification of pseudoknotted ribozymes.RNA (New York, N.Y.) · 2023Article
- On the early identification and characterization of pear blister canker viroid, apple dimple fruit viroid, peach latent mosaic viroid and chrysanthemum chlorotic mottle viroid.Virus research · 2023Article
- 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
- The hammerhead self-cleaving motif as a precursor to complex endonucleolytic ribozymes.RNA (New York, N.Y.) · 2021Article
- Hovlinc is a recently evolved class of ribozyme found in human lncRNA.Nature chemical biology · 2021Article
- A cell-based ribozyme reporter system employing a chromosomally-integrated 5' exonuclease gene.BMC molecular and cell biology · 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
- Article
- Intracellular selection of trans-cleaving hammerhead ribozymes.Nucleic acids research · 2019Article
- Highly motif- and organism-dependent effects of naturally occurring hammerhead ribozyme sequences on gene expression.RNA biology · 2018Article
- Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers.RNA biology · 2017Article
- Circular RNAs with hammerhead ribozymes encoded in eukaryotic genomes: The enemy at home.RNA biology · 2017Article
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3 authors.
Funding
Abstract
Deep sequencing of viral or bacterial nucleic acids monitors the presence and diversity of microbes in select populations and locations. Metagenomic study of mammalian viromes can help trace paths of viral transmissions within or between species. High throughput sequencing of patient and untreated sewage microbiomes showed many sequences with no similarity to genomic sequences of known function or origin. To estimate the distribution of functional RNAs in these microbiomes, we used the hammerhead ribozyme (HHR) motif to search for sequences capable of assuming its three-way junction fold. Although only two of the three possible natural HHR topologies had been known, our analysis revealed highly active ribozymes that terminated in any of the three stems. The most abundant of these are type II HHRs, one of which is the fastest natural cis-acting HHR yet discovered. Altogether, 13 ribozymes were confirmed in vitro, but only one showed sequence similarity to previously described HHRs. Sequences surrounding the ribozymes do not generally show similarity to known genes, except in one case, where a ribozyme is immediately preceded by a bacterial RadC gene. We demonstrate that a structure-based search for a known functional RNA is a powerful tool for analysis of metagenomic datasets, complementing sequence alignments.
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