ArticleNucleic acids research2006
Computer simulation of chaperone effects of Archaeal C/D box sRNA binding on rRNA folding.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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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.
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Who cites it
9 citing papers in PubMed, 15 citations in OpenAlex.
- Conservation of Archaeal C/D Box sRNA-Guided RNA Modifications.Frontiers in microbiology · 2021Review
- Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species.Nucleic acids research · 2018Article
- Partial methylation at Am100 in 18S rRNA of baker's yeast reveals ribosome heterogeneity on the level of eukaryotic rRNA modification.PloS one · 2014Article
- On the importance of cotranscriptional RNA structure formation.RNA (New York, N.Y.) · 2013Review
- COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account.Nucleic acids research · 2013Article
- Generation of a mouse model with down-regulated U50 snoRNA (SNORD50) expression and its organ-specific phenotypic modulation.PloS one · 2013Article
- Ribonucleoproteins in archaeal pre-rRNA processing and modification.Archaea (Vancouver, B.C.) · 2013Review
- An overview of the introns-first theory.Journal of molecular evolution · 2009Article
- Functional importance of individual rRNA 2'-O-ribose methylations revealed by high-resolution phenotyping.RNA (New York, N.Y.) · 2008Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Archaeal C/D box small RNAs (sRNAs) are homologues of eukaryotic C/D box small nucleolar RNAs (snoRNAs). Their main function is guiding 2'-O-ribose methylation of nucleotides in rRNAs. The methylation requires the pairing of an sRNA antisense element to an rRNA target site with formation of an RNA-RNA duplex. The temporary formation of such a duplex during rRNA maturation is expected to influence rRNA folding in a chaperone-like way, in particular in thermophilic Archaea, where multiple sRNAs with two binding sites are found. Here we investigate possible mechanisms of chaperone function of Archaeoglobus fulgidus and Pyrococcus abyssi C/D box sRNAs using computer simulations of rRNA secondary structure formation by genetic algorithm. The effects of sRNA binding on rRNA structure are introduced as temporary structural constraints during co-transcriptional folding. Comparisons of the final predictions with simulations without sRNA binding and with phylogenetic structures show that sRNAs with two antisense elements may significantly facilitate the correct formation of long-range interactions in rRNAs, in particular at elevated temperatures. The simulations suggest that the main mechanism of this effect is a transient restriction of folding in rRNA domains where the termini are brought together by binding to double-guide sRNAs.
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