A Method for Rapid Inducible RNA Decay.

Lauren A Blake, Leslie Watkins, Bin Wu

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

3 authors.

Lauren A BlakeDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

Leslie WatkinsDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

Bin WuDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA. bwu20@jhmi.edu.

Funding

Biochemistry, Cellular and Molecular Biology Program: JHU BioGREAT (Biomedical Graduate REsiliency & Adaptability Training)T32GM144272 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Takanari Inoue · 2022 to 2026

$5.4M

Developing optogenetic and chemogenetic approaches to control RNA metabolism in live cellsR01GM136897 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI WU, BIN · 2021 to 2024

$1.8M

NIGMS NIH HHS R01 GM136897NIGMS NIH HHS T32 GM144272

6 · The paper itself

Abstract

Modulating RNA decay is a powerful tool to investigate RNA degradation dynamics. Here, we describe a protocol to inducibly recruit protein factors to regulate target RNA metabolism, called Rapid Inducible Decay of RNA (RIDR). RIDR induces fast and synchronous decay of target mRNAs within minutes and enables direct visualization of mRNA decay dynamics and subcellular kinetics in living cells. Here, we provide detailed procedures to make stable cell lines, conduct fixed- and live-cell measurements, and perform data analysis. We discuss the potential pitfalls and make RIDR applicable to a general biology lab.

Indexed as

RNA, MessengerRNA StabilityCell LineHumansKineticsRNA, MessengerFluorescent in situ hybridizationImmunofluorescenceKineticsRNA decaySingle molecule imaging

Identifiers

PMID39535712

DOI10.1007/978-1-0716-4176-7_13

PMCPMC11874224

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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.