ArticleRNA (New York, N.Y.)2015
Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics.
Article in RNA (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed, 39 citations in OpenAlex.
- Mutations in apicoplast rRNA genes are associated with clindamycin resistance and impair the ability of malaria parasites to infect mosquitoes.Antimicrobial agents and chemotherapy · 2026Article
- Evidence for strong purifying selection of humanProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Structure of an archaeal ribosome reveals a divergent active site and hibernation factor.Nature microbiology · 2025Article
- The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.Nature communications · 2024Article
- Article
- RiboXYZ: a comprehensive database for visualizing and analyzing ribosome structures.Nucleic acids research · 2023Article
- Article
- A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome and its significance for the elongation cycle kinetics.Computational and structural biotechnology journal · 2023Article
- Computationally-guided design and selection of high performing ribosomal active site mutants.Nucleic acids research · 2022Article
- Varying strength of selection contributes to the intragenomic diversity of rRNA genes.Nature communications · 2022Article
- Photorhabdus antibacterial Rhs polymorphic toxin inhibits translation through ADP-ribosylation of 23S ribosomal RNA.Nucleic acids research · 2021Article
- The role of lncRNAs in innate immunity and inflammation.RNA biology · 2021Review
- Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM.Molecules (Basel, Switzerland) · 2020Review
- RNA sectors and allosteric function within the ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The 23S Ribosomal RNA FromFrontiers in microbiology · 2020Article
- SHAPE Probing Reveals Human rRNAs Are Largely Unfolded in Solution.Biochemistry · 2019Article
- Differences in the path to exit the ribosome across the three domains of life.Nucleic acids research · 2019Article
- Small Non-Coding RNAs Derived From Eukaryotic Ribosomal RNA.Non-coding RNA · 2019Review
- Translation: The Universal Structural Core of Life.Molecular biology and evolution · 2018Article
- Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing.Nucleic acids research · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Comparative analysis of ribosomal RNA (rRNA) sequences has elucidated phylogenetic relationships. However, this powerful approach has not been fully exploited to address ribosome function. Here we identify stretches of evolutionarily conserved sequences, which correspond with regions of high functional importance. For this, we developed a structurally aligned database, FLORA (full-length organismal rRNA alignment) to identify highly conserved nucleotide elements (CNEs) in 23S-28S rRNA from each phylogenetic domain (Eukarya, Bacteria, and Archaea). Universal CNEs (uCNEs) are conserved in sequence and structural position in all three domains. Those in regions known to be essential for translation validate our approach. Importantly, some uCNEs reside in areas of unknown function, thus identifying novel sequences of likely great importance. In contrast to uCNEs, domain-specific CNEs (dsCNEs) are conserved in just one phylogenetic domain. This is the first report of conserved sequence elements in rRNA that are domain-specific; they are largely a eukaryotic phenomenon. The locations of the eukaryotic dsCNEs within the structure of the ribosome suggest they may function in nascent polypeptide transit through the ribosome tunnel and in tRNA exit from the ribosome. Our findings provide insights and a resource for ribosome function studies.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.