Evidence map›Paper›PMID 39392747›Full record

ArticleSTAR protocols2024

Protocols for identifying endogenous interactors of RNA-binding proteins in mammalian cells using the peroxidase APEX2 biotin-labeling method.

Ryota Uozumi, Kohji Mori, Shoshin Akamine, Manabu Ikeda

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 2024. 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. 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

4 authors.

Ryota UozumiDepartment of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.
Kohji MoriDepartment of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan. Electronic address: kmori@psy.med.osaka-u.ac.jp.
Shoshin AkamineDepartment of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.
Manabu IkedaDepartment of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Engineered ascorbate peroxidase, APEX2, is widely applied for the identification of intracellular molecule-molecule interaction analyses. Here, we present a protocol for identifying interactors of RNA-binding proteins (RBPs) in living HeLa cells using the APEX2 fusion construct. We describe steps for generation of RBP-APEX2, proximity biotin labeling, and preparation of labeled molecules for mass spectrometry analysis. This protocol may be applicable to other cell cultures and RBPs of interest. For complete details on the use and execution of this protocol, please refer to Uozumi et al.

Indexed as

BiotinDNA-(Apurinic or Apyrimidinic Site) LyaseRNA-Binding ProteinsAscorbate PeroxidasesBiotinylationEndonucleasesHeLa CellsHumansMass SpectrometryMultifunctional EnzymesStaining and LabelingAPEX2 protein, humanAscorbate PeroxidasesBiotinDNA-(Apurinic or Apyrimidinic Site) LyaseEndonucleasesMultifunctional EnzymesRNA-Binding ProteinsBioinformaticsCell BiologyProtein expression and purificationProteomics

Identifiers

PMID39392747
PMCPMC11736044

What OpenQuestion holds

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LicenceCC BY-NC-ND
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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.