Evidence map›Paper›PMID 40540402›Full record

ReviewCell reports2025

A molecular cartographer's toolkit for mapping RNA's uncharted realms.

Faraz K Mardakheh, David M Shechner

Abstract readReview
In one paragraph

Review in Cell reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
  4. Article
  5. Review
  6. 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

2 authors.

Faraz K MardakhehDepartment of Biochemistry, University of Oxford, South Parks Road, Oxford, UK. Electronic address: faraz.mardakheh@bioch.ox.ac.uk.
David M ShechnerDepartment of Pharmacology, University of Washington, Seattle, WA, USA; Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA. Electronic address: shechner@uw.edu.

Funding

Function, composition, and mechanism of RNA splicing factories in cardiomyopathyR01HL160825 · NHLBI · UNIVERSITY OF WASHINGTON · PI Charles E Murry · 2023 to 2026
$2.3M
Oligonucleotide-directed in situ proximity biotinylation: a unified method for mapping RNA-interacting proteomes, transcriptomes and genomic loci within intact cells.R01GM138799 · NIGMS · UNIVERSITY OF WASHINGTON · PI SHECHNER, DAVID MICHAEL · 2020 to 2024
$1.7M
NHLBI NIH HHS R01 HL160825NIGMS NIH HHS R01 GM138799
6 · The paper itself

Abstract

Deciphering RNA molecules' function and regulation requires an in-depth understanding of the myriad interactions these RNAs form within their cellular environment. In this review, we present a comprehensive overview of recent technological advances that collectively form a molecular toolkit for mapping the molecular environment of RNA. We discuss innovative RNA-centric methods designed to overcome long-standing challenges in capturing direct RNA-protein interactions in living cells. Additionally, we explore transformative proximity-labeling techniques that leverage engineered enzymes and chemical catalysts to spatially resolve the composition of RNA-associated microenvironments. By critically evaluating the strengths and limitations of these emerging methodologies, we highlight how they are reshaping our understanding of RNA function, from local binding events to the dynamic organization of RNA-scaffolded compartments. These advancements not only promise to elucidate the molecular grammar underlying RNA regulatory networks in unprecedented details but also pave the way for an integrative, system-level understanding of complex RNA-mediated cellular processes.

Indexed as

RNAAnimalsHumansRNA-Binding ProteinsRNARNA-Binding Proteinsbiotechnology developmentCP: Molecular biologymicroenvironment mappingRNA-binding proteinsRNA localization

Identifiers

PMID40540402
PMCPMC12320716

What OpenQuestion holds

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LicenceCC BY-NC
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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.