Evidence map›Paper›PMID 35922633›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2022

Toeprint Assays for Detecting RNA Structure and Protein-RNA Interactions.

Helen Yakhnin, Paul Babitzke

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. Multitier regulation of theJournal of bacteriology · 2024
    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

2 authors.

Helen YakhninDepartment of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Paul BabitzkeDepartment of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA. pxb28@psu.edu.

Funding

Mechanism of CsrA-mediated global regulationR01GM059969 · NIGMS · UNIVERSITY OF NORTH TEXAS HLTH SCI CTR · PI BABITZKE, PAUL L, ROMEO, TONY · 1999 to 2021
$7.6M
Regulation of transcription elongationR01GM098399 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI BABITZKE, PAUL L · 2012 to 2024
$3.6M
NIGMS NIH HHS R01 GM059969NIGMS NIH HHS R01 GM098399
6 · The paper itself

Abstract

Toeprint assays are primer extension inhibition assays that can detect the 3' end of an RNA secondary structure, the position of a bound RNA binding protein, as well as the position of a bound 30S ribosomal subunit or a stalled ribosome. Here we describe how this assay was used to identify an RNA hairpin that sequesters a Shine-Dalgarno sequence, how the RNA-binding protein CsrA can alter RNA structure and affect 30S ribosomal subunit binding, and how the macrolide antibiotic tylosin can induce ribosome stalling.

Indexed as

Escherichia coli ProteinsEscherichia coliGene Expression Regulation, BacterialProtein BiosynthesisRepressor ProteinsRibosomesRNARNA-Binding ProteinsCsrA protein, E coliEscherichia coli ProteinsRepressor ProteinsRNARNA-Binding ProteinsPrimer extension inhibitionProtein–RNA interactionRibosomeRNA structureToeprintTranslational control

Identifiers

PMID35922633
PMCPMC9426256

What OpenQuestion holds

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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.