ArticleRNA (New York, N.Y.)2012
Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features.
Article in RNA (New York, N.Y.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 29 citations in OpenAlex.
- A pseudouridine-related prognostic model of colorectal cancer based on single-cell sequencing analysis and transcriptome analysis.Scientific reports · 2026Article
- Investigation of the global translational response to oxidative stress in the model archaeonmSphere · 2025Article
- Non-conserved microRNAs and their roles in plants: the case for legumes.Plant biology (Stuttgart, Germany) · 2025Review
- Landscape of RNA pseudouridylation in archaeon Sulfolobus islandicus.Nucleic acids research · 2024Article
- Aging-induced pseudouridine synthase 10 impairs hematopoietic stem cells.Haematologica · 2023Article
- H/ACA Small Ribonucleoproteins: Structural and Functional Comparison Between Archaea and Eukaryotes.Frontiers in microbiology · 2021Review
- The presence of the ACA box in archaeal H/ACA guide RNAs promotes atypical pseudouridylation.RNA (New York, N.Y.) · 2020Article
- Small RNAs of Haloferax mediterranei: Identification and Potential Involvement in Nitrogen Metabolism.Genes · 2018Article
- Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea.Nucleic acids research · 2015Article
- Capture, Unfolding, and Detection of Individual tRNA Molecules Using a Nanopore Device.Frontiers in bioengineering and biotechnology · 2015Article
- Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis.BMC genomics · 2014Article
- RNA-guided isomerization of uridine to pseudouridine--pseudouridylation.RNA biology · 2014Review
- Small regulatory RNAs in Archaea.RNA biology · 2014Review
- RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.RNA biology · 2013Article
- RNA pseudouridylation: new insights into an old modification.Trends in biochemical sciences · 2013Review
- Ribonucleoproteins in archaeal pre-rRNA processing and modification.Archaea (Vancouver, B.C.) · 2013Review
- Abstracts of the 11th Annual UT-ORNL-KBRIN Bioinformatics Summit 2012. Louisville, Kentucky, USA. March 30-April 1, 2012.BMC bioinformatics · 2012Article
- Complete genome sequence of Pyrobaculum oguniense.Standards in genomic sciences · 2012Article
- RNA processing in the minimal organism Nanoarchaeum equitans.Genome biology · 2012Article
- Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species.Frontiers in microbiology · 2012Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the Eukarya and Archaea, small RNA-guided pseudouridine modification is believed to be an essential step in ribosomal RNA maturation. While readily modeled and identified by computational methods in eukaryotic species, these guide RNAs have not been found in most archaeal genomes. Using high-throughput transcriptome sequencing and comparative genomics, we have identified ten novel small RNA families that appear to function as H/ACA pseudouridylation guide sRNAs, yet surprisingly lack several expected canonical features. The new RNA genes are transcribed and highly conserved across at least six species in the archaeal hyperthermophilic genus Pyrobaculum. The sRNAs exhibit a single hairpin structure interrupted by a conserved kink-turn motif, yet only two of ten families contain the complete canonical structure found in all other H/ACA sRNAs. Half of the sRNAs lack the conserved 3'-terminal ACA sequence, and many contain only a single 3' guide region rather than the canonical 5' and 3' bipartite guides. The predicted sRNA structures contain guide sequences that exhibit strong complementarity to ribosomal RNA or transfer RNA. Most of the predicted targets of pseudouridine modification are structurally equivalent to those known in other species. One sRNA appears capable of guiding pseudouridine modification at positions U54 and U55 in most or all Pyrobaculum tRNAs. We experimentally tested seven predicted pseudouridine modifications in ribosomal RNA, and all but one was confirmed. The structural insights provided by this new set of Pyrobaculum sRNAs will augment existing models and may facilitate the identification and characterization of new guide sRNAs in other archaeal species.
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