Evidence map›Paper›PMID 29864677›Full record

ArticleVirology2018

SELEX and SHAPE reveal that sequence motifs and an extended hairpin in the 5' portion of Turnip crinkle virus satellite RNA C mediate fitness in plants.

Charlie F Bayne, Max E Widawski, Feng Gao, Mohammed H Masab, Maitreyi Chattopadhyay, Allison M Murawski, Robert M Sansevere, Bryan D Lerner, Rinaldys J Castillo, Trevor Griesman and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Virology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
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

1 citing paper in PubMed.

  1. Review
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

15 authors.

Charlie F BayneDepartment of Biology, Dickinson College, Carlisle, PA 17013, USA.
Max E WidawskiDepartment of Biology, Dickinson College, Carlisle, PA 17013, USA.
Feng GaoDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
Mohammed H MasabDepartment of Biology, Dickinson College, Carlisle, PA 17013, USA.
Maitreyi ChattopadhyayDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
Allison M MurawskiDepartment of Biology, Dickinson College, Carlisle, PA 17013, USA.
Robert M SansevereDepartment of Biology, Dickinson College, Carlisle, PA 17013, USA.
Bryan D LernerDepartment of Biology, Dickinson College, Carlisle, PA 17013, USA.
Rinaldys J CastilloDepartment of Biology, Dickinson College, Carlisle, PA 17013, USA.
Trevor GriesmanDepartment of Biology, Dickinson College, Carlisle, PA 17013, USA.
Jiantao FuDepartment of Biology, Dickinson College, Carlisle, PA 17013, USA.
Jennifer K HibbenDepartment of Biology, Dickinson College, Carlisle, PA 17013, USA.
Alma D Garcia-PerezDepartment of Biology, Dickinson College, Carlisle, PA 17013, USA.
Anne E SimonDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
David B KushnerDepartment of Biology, Dickinson College, Carlisle, PA 17013, USA. Electronic address: kushnerd@dickinson.edu.

Funding

Graduate Training in VirologyT32AI125186 · NIAID · UNIV OF MARYLAND, COLLEGE PARK · PI SIMON, ANNE ELIZABETH · 2016 to 2020
$1.3M
New Paradigms for Ribosome Recoding in (+)Strand VirusesR21AI117882 · NIAID · UNIV OF MARYLAND, COLLEGE PARK · PI SIMON, ANNE ELIZABETH · 2015 to 2016
$410k
NIAID NIH HHS R21 AI117882NIAID NIH HHS T32 AI125186
6 · The paper itself

Abstract

Noncoding RNAs use their sequence and/or structure to mediate function(s). The 5' portion (166 nt) of the 356-nt noncoding satellite RNA C (satC) of Turnip crinkle virus (TCV) was previously modeled to contain a central region with two stem-loops (H6 and H7) and a large connecting hairpin (H2). We now report that in vivo functional selection (SELEX) experiments assessing sequence/structure requirements in H2, H6, and H7 reveal that H6 loop sequence motifs were recovered at nonrandom rates and only some residues are proposed to base-pair with accessible complementary sequences within the 5' central region. In vitro SHAPE of SELEX winners indicates that the central region is heavily base-paired, such that along with the lower stem and H2 region, one extensive hairpin exists composing the entire 5' region. As these SELEX winners are highly fit, these characteristics facilitate satRNA amplification in association with TCV in plants.

Indexed as

Evolution, MolecularCarmovirusNucleic Acid ConformationPlantsRNA, SatelliteRNA, ViralSELEX Aptamer TechniqueVirus ReplicationRNA, SatelliteRNA, ViralRNA evolutionRNA structureSatellite RNASELEXTurnip crinkle virus

Identifiers

PMID29864677
PMCPMC6042292

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Registered trials

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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.