ArticleRNA (New York, N.Y.)2012
Kinetic analysis of pre-ribosome structure in vivo.
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 19 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
19 citing papers in PubMed, 28 citations in OpenAlex.
- In vivo structure profiling reveals human cytosolic and mitochondrial tRNA structurome and interactome in response to stress.Nature communications · 2025Article
- Mapping snoRNA-target RNA interactions in an RNA-binding protein-dependent manner with chimeric eCLIP.Genome biology · 2025Article
- Non-radioactive In Vivo Labeling of RNA with 4-Thiouracil.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy.RNA (New York, N.Y.) · 2020Article
- Gaining insight into transcriptome-wide RNA population dynamics through the chemistry of 4-thiouridine.Wiley interdisciplinary reviews. RNA · 2019Review
- RNA helicases mediate structural transitions and compositional changes in pre-ribosomal complexes.Nature communications · 2018Article
- Viewing pre-60S maturation at a minute's timescale.Nucleic acids research · 2018Article
- Toward Time-Resolved Analysis of RNA Metabolism in Archaea Using 4-Thiouracil.Frontiers in microbiology · 2017Article
- Probing the structure of ribosome assembly intermediates in vivo using DMS and hydroxyl radical footprinting.Methods (San Diego, Calif.) · 2016Article
- Progress and challenges for chemical probing of RNA structure inside living cells.Nature chemical biology · 2015Review
- In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote formation of the central pseudoknot.PLoS biology · 2015Article
- Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution.Nucleic acids research · 2014Article
- A pre-ribosomal RNA interaction network involving snoRNAs and the Rok1 helicase.RNA (New York, N.Y.) · 2014Article
- Ribosome RNA assembly intermediates visualized in living cells.Biochemistry · 2014Article
- RNA mimicry by the fap7 adenylate kinase in ribosome biogenesis.PLoS biology · 2014Article
- Imp3 unfolds stem structures in pre-rRNA and U3 snoRNA to form a duplex essential for small subunit processing.RNA (New York, N.Y.) · 2013Article
- A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs.Cell · 2013Article
- COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account.Nucleic acids research · 2013Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Pre-ribosomal particles undergo numerous structural changes during maturation, but their high complexity and short lifetimes make these changes very difficult to follow in vivo. In consequence, pre-ribosome structure and composition have largely been inferred from purified particles and analyzed in vitro. Here we describe techniques for kinetic analyses of the changes in pre-ribosome structure in living cells of Saccharomyces cerevisiae. To allow this, in vivo structure probing by DMS modification was combined with affinity purification of newly synthesized 20S pre-rRNA over a time course of metabolic labeling with 4-thiouracil. To demonstrate that this approach is generally applicable, we initially analyzed the accessibility of the region surrounding cleavage site D site at the 3' end of the mature 18S rRNA region of the pre-rRNA. This revealed a remarkably flexible structure throughout 40S subunit biogenesis, with little stable RNA-protein interaction apparent. Analysis of folding in the region of the 18S central pseudoknot was consistent with previous data showing U3 snoRNA-18S rRNA interactions. Dynamic changes in the structure of the hinge between helix 28 (H28) and H44 of pre-18S rRNA were consistent with recently reported interactions with the 3' guide region of U3 snoRNA. Finally, analysis of the H18 region indicates that the RNA structure matures early, but additional protection appears subsequently, presumably reflecting protein binding. The structural analyses described here were performed on total, affinity-purified, newly synthesized RNA, so many classes of RNA and RNA-protein complex are potentially amenable to this approach.
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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.