Evidence map›Paper›PMID 40913182›Full record

ArticleNature genetics2025

Genetic variants affecting RNA stability influence complex traits and disease risk.

Elaine Huang, Ting Fu, Ling Zhang, Guanao Yan, Ryo Yamamoto, Sari Terrazas, Thuy Linh Nguyen, Carlos Gonzalez-Figueroa, Armen Khanbabaei, Jae Hoon Bahn and 8 more

Abstract read
PubMed Publisher
In one paragraph

Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

  1. Article
  2. The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026
    Article
  3. Article
  4. Article
  5. Article
  6. Disruption of a six-nucleotide miRNA motif improvesbioRxiv : the preprint server for biology · 2025
    Article
  7. 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

18 authors.

Elaine HuangBioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0003-2057-934X
Ting FuDepartment of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0003-0936-732X
Ling ZhangDepartment of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA.
Guanao YanDepartment of Statistics and Data Science, University of California, Los Angeles, CA, USA.
Ryo YamamotoBioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0003-3134-145X
Sari TerrazasMolecular Biology Interdepartmental Program, University of California, Los Angeles, CA, USA.
Thuy Linh NguyenDepartment of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA.
Carlos Gonzalez-FigueroaDepartment of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA.
Armen KhanbabaeiMolecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0002-2316-2892
Jae Hoon BahnDepartment of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA.
Rajagopal VaradaDepartment of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0001-6740-6564
Kofi AmoahBioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.
Jonatan HervosoBioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.
Michelle T PaulsenCenter for RNA Biomedicine and Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
Brian MagnusonDepartment of Pathology, University of Michigan, Ann Arbor, MI, USA.
Mats LjungmanCenter for RNA Biomedicine and Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.ORCID http://orcid.org/0000-0003-1553-6695
Jingyi Jessica LiBioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0002-9288-5648
Xinshu XiaoBioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA. gxxiao@ucla.edu.ORCID http://orcid.org/0000-0002-9362-8029

Funding

Research Training in Cell and Molecular BiologyT32GM145388 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Jorge Torres · 2022 to 2026
$5.2M
Analysis of functional genetic variants in RNA processing and expressionU01HG009417 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI XIAO, XINSHU GRACE · 2017 to 2021
$3.2M
Systematic analysis of functional 3’ UTR genetic variants and their relevance to Alzheimer’s DiseaseR01AG075206 · NIA · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Xinshu Grace Xiao · 2022 to 2026
$2.7M
U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) HG009382U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) U01HG009417U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) T32GM145388U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging) R01AG075206
6 · The paper itself

Abstract

Gene expression is modulated jointly by transcriptional regulation and messenger RNA stability, yet the latter is often overlooked in studies on genetic variants. Here, leveraging metabolic labeling data (Bru/BruChase-seq) and a new computational pipeline, RNAtracker, we categorize genes as allele-specific RNA stability (asRS) or allele-specific RNA transcription events. We identify more than 5,000 asRS variants among 665 genes across a panel of 11 human cell lines. These variants directly overlap conserved microRNA target regions and allele-specific RNA-binding protein sites, illuminating mechanisms through which stability is mediated. Furthermore, we identified causal asRS variants using a massively parallel screen (MapUTR) for variants that affect post-transcriptional mRNA abundance, as well as through CRISPR prime editing approaches. Notably, asRS genes were enriched significantly among a multitude of immune-related pathways and contribute to the risk of several immune system diseases. This work highlights RNA stability as a critical, yet understudied mechanism linking genetic variation and disease.

Indexed as

Genetic Predisposition to DiseaseGenetic VariationMultifactorial InheritanceRNA StabilityAllelesCell LineGene Expression RegulationHumansMicroRNAsPolymorphism, Single NucleotideRNA, MessengerMicroRNAsRNA, Messenger

Identifiers

PMID40913182

What Socratic holds

Textmetadata
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 Socratic graph.