Evidence map›Paper›PMID 25752599›Full record

ArticleRNA (New York, N.Y.)2015

Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy.

Rees F Garmann, Ajaykumar Gopal, Shreyas S Athavale, Charles M Knobler, William M Gelbart, Stephen C Harvey

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

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 28 papers.

0numbers the graph read from it
0cells of the map it votes in
28citing papers in PubMed
3.5field-weighted citation impact, top 7% of its field
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

28 citing papers in PubMed, 49 citations in OpenAlex.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Viral RNA structure analysis using DMS-MaPseq.Methods (San Diego, Calif.) · 2020
    Review
  10. Article
  11. Article
  12. Review
  13. Review
  14. Review
  15. Article
  16. Compactness of viral genomes: effect of disperse and localized random mutations.Journal of physics. Condensed matter : an Institute of Physics journal · 2018
    Article
  17. Article
  18. Article
  19. Article
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors at 2 institutions in 1 country.

Rees F GarmannDepartment of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA.
Ajaykumar GopalDepartment of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA.
Shreyas S AthavaleSchool of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
Charles M KnoblerDepartment of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA.
William M GelbartDepartment of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA.
Stephen C HarveySchool of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
University of California, Los Angeles · USGeorgia Institute of Technology · US

Funding

Packaging and Structure of Viral GenomesR01GM070785 · NIGMS · GEORGIA INSTITUTE OF TECHNOLOGY · PI HARVEY, STEPHEN C. · 2004 to 2011
$2.0M
HIGH-END CRYOEM INSTRUMENT FOR UCLA ELECTRON IMAGING CTR FOR NANOMACHINES: AIDSS10RR023057 · NCRR · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ZHOU, Z HONG · 2006 to 2006
$1.6M
NCRR NIH HHS 1S10RR23057NCRR NIH HHS S10 RR023057NIGMS NIH HHS R01 GM070785NIGMS NIH HHS R01 GM70785
6 · The paper itself

Abstract

The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures.

Indexed as

Genome, ViralNucleic Acid ConformationAlgorithmsComputational BiologyCryoelectron MicroscopyMolecular ConformationRNA, ViralTobacco mosaic satellite virusRNA, Viralcryo-electron microscopysecondary structureviral RNA genome

Identifiers

PMID25752599
PMCPMC4408795
OpenAlexW2133267130

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

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.