Evidence map›Paper›PMID 39661502›Full record

ArticleSTAR protocols2024

Molecular protocol for genome-wide and cell-type-selective profiling of in vivo small noncoding RNA:target RNA interactions by CIMERA-seq.

Xinbei Li, Emily A Eiss, William T Mills, Mollie K Meffert

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. 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

4 authors.

Xinbei LiDepartment of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Emily A EissDepartment of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
William T MillsDepartment of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Mollie K MeffertDepartment of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address: mkm@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
Defining post-transcriptional gene regulation in FMRP-deficiency usingmiRNA:target chimerasR01MH129292 · NIMH · JOHNS HOPKINS UNIVERSITY · PI MOLLIE Katherine MEFFERT · 2023 to 2026
$1.9M
Characterizing the regulatory roles of microRNA on mitochondria in the mammalian CNSF31MH136717 · NIMH · JOHNS HOPKINS UNIVERSITY · PI Emily Eiss · 2024 to 2026
$141k
Using microRNA-target chimeras to study post-transcriptional gene regulation in the mammalian CNSF31MH124282 · NIMH · JOHNS HOPKINS UNIVERSITY · PI MILLS, WILLIAM THOMAS · 2021 to 2023
$123k
NIGMS NIH HHS T32 GM144272NIMH NIH HHS F31 MH124282NIMH NIH HHS F31 MH136717NIMH NIH HHS R01 MH129292
6 · The paper itself

Abstract

Small noncoding RNAs (sncRNAs) can regulate gene expression by guiding the RNA-induced silencing complex (RISC) to targeted transcripts for translational repression and/or target destabilization. Here, we present a robust benchtop protocol, termed CIMERA-seq, for the unambiguous profiling of sncRNA:target RNA interactions in a genome-wide and cell-type-selective manner. We describe steps for in vivo crosslinking and harvesting tissue, immunoprecipitation and covalent ligation of sncRNAs to target RNAs within the RISC, and sequencing of the resulting chimeric sncRNA:target RNA interactions. For complete details on the use and execution of this protocol, please refer to Li et al.

Indexed as

RNA, Small UntranslatedAnimalsHumansImmunoprecipitationMiceRNA-Induced Silencing ComplexSequence Analysis, RNARNA-Induced Silencing ComplexRNA, Small UntranslatedMolecular BiologyNeuroscienceProtein Biochemistry

Identifiers

PMID39661502
PMCPMC11697689

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.