Evidence map›Paper›PMID 40250958›Full record

ArticleMethods in enzymology2025

Identification of RBP binding sites using RNA deaminases.

Tao Yu, Qishan Liang, Shuhao Xu, Gene W Yeo

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Methods in enzymology, 2025. 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. 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

4 authors.

Tao YuDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, United States; Sanford Stem Cell Institute and Stem Cell Program, University of California San Diego, La Jolla, CA, United States; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, United States; Center for RNA Technologies and Therapeutics, University of California San Diego, La Jolla, CA, United States.
Qishan LiangDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, United States; Sanford Stem Cell Institute and Stem Cell Program, University of California San Diego, La Jolla, CA, United States; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, United States; Center for RNA Technologies and Therapeutics, University of California San Diego, La Jolla, CA, United States.
Shuhao XuDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, United States; Sanford Stem Cell Institute and Stem Cell Program, University of California San Diego, La Jolla, CA, United States; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, United States.
Gene W YeoDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, United States; Sanford Stem Cell Institute and Stem Cell Program, University of California San Diego, La Jolla, CA, United States; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, United States; Center for RNA Technologies and Therapeutics, University of California San Diego, La Jolla, CA, United States; Sanford Laboratories for Innovative Medicines, La Jolla, CA, United States. Electronic address: geneyeo@ucsd.edu.

Funding

Functional RNA elements in the human genomeR01HG004659 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Kevin Daniel Corbett, Eugene Wei-Ming Yeo · 2008 to 2026
$12.4M
A comprehensive binding and functional map of human RNA-binding proteinsU24HG009889 · NHGRI · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI GRAVELEY, BRENTON R., YEO, EUGENE WEI-MING · 2022 to 2025
$5.5M
STAMP technology to enable single-cell and isoform-sensitive detection of RBP sitesR01HG011864 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI YEO, EUGENE WEI-MING · 2021 to 2024
$4.0M
Ribo-STAMPEDE: novel tools for molecular profiling of brain cell typesRF1MH126719 · NIMH · SCRIPPS RESEARCH INSTITUTE, THE · PI LIPPI, GIORDANO, YEO, EUGENE WEI-MING · 2022 to 2022
$2.3M
Illumina NovaSeq 6000 Sequencing SystemS10OD026929 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI JEPSEN, KRISTEN LYNN · 2019 to 2019
$600k
NHGRI NIH HHS R01 HG004659NHGRI NIH HHS R01 HG011864NHGRI NIH HHS U24 HG009889NIH HHS S10 OD026929NIMH NIH HHS RF1 MH126719
6 · The paper itself

Abstract

RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing. Identification of their binding sites has important implications for their physiological and disease-related functions. Crosslinking and immunoprecipitation, followed by sequencing (CLIP-seq) and its derivatives, are the most commonly used methods to identify RBP binding sites, but are laborious and require a large amount of starting material. Recent advancements harnessing RNA deaminases in fusion to any RBP of interest, allow for the profiling of RBP binding sites from low-input samples in simpler procedures. Among these efforts, we developed STAMP (Surveying Targets by APOBEC-Mediated Profiling), which efficiently detects RBP-RNA interactions. This chapter describes the detailed protocol for the STAMP method, including plasmid construction, delivery and sorting, library preparation and bioinformatic data analysis.

Indexed as

RNARNA-Binding ProteinsBinding SitesComputational BiologyGene LibraryHumansImmunoprecipitationProtein BindingSequence Analysis, RNARNARNA-Binding ProteinsAPOBEC1RNA-binding proteinRNA deaminaseRNA sequencing

Identifiers

PMID40250958
PMCPMC12333437

What OpenQuestion holds

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Read underepoch 390

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.