Evidence map›Paper›PMID 42458539›Full record

ArticleGenome biology2026

Uncovering the isoform-resolution kinetic landscape of nonsense-mediated mRNA decay with EZbakR.

Justin W Mabin, Isaac W Vock, Martin Machyna, Nazmul Haque, Poonam Thakran, Alexandra Zhang, Ganesha Rai, Isabelle Nathalie-Marie Leibler, James Inglese, Matthew D Simon and 1 more

Abstract read
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In one paragraph

Article in Genome biology, 2026. 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.

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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Justin W Mabin *Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Isaac W Vock *Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
Martin MachynaDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
Nazmul HaqueBiochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Poonam ThakranBiochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Alexandra ZhangDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
Ganesha RaiNational Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA.
Isabelle Nathalie-Marie LeiblerNational Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA.
James IngleseNational Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA.
Matthew D SimonDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
J Robert HoggBiochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA. j.hogg@nih.gov.ORCID https://orcid.org/0000-0001-5729-5135

Funding

Phenotypic Assay Design and Development for Rare and Neglected DiseasesZIATR000052 · NCATS · NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES · PI INGLESE, JAMES · 2015 to 2025
$3.7M
Revealing the dynamics of RNA metabolism with nucleotide recoding chemistryR01GM137117 · NIGMS · YALE UNIVERSITY · PI Matthew David Simon · 2020 to 2026
$2.6M
National Heart Lung and Blood Institute ZIAHL006158NCATS NIH HHS ZIATR000052NIGMS NIH HHS R01GM137117
6 · The paper itself

Abstract

Cellular RNA abundance reflects synthesis and decay rates, which can differ among transcripts of the same gene. Understanding nonsense-mediated mRNA decay and other RNA turnover pathways requires isoform-resolved kinetic measurements, but existing bioinformatic tools cannot robustly estimate isoform-specific degradation rate constants. We extend the EZbakR-suite to infer isoform-level kinetics from nucleotide-recoding RNA-seq data, uncovering unexpected variability in nonsense-mediated decay efficiency among transcripts with premature termination codons and rapid decay of select mRNAs lacking premature termination codons. Our findings highlight the competition between nonsense-mediated decay and other decay pathways and provide mechanistic insights into transcript features promoting efficient decay.

Indexed as

Nonsense Mediated mRNA DecayRNA, MessengerCodon, NonsenseHumansKineticsCodon, NonsenseRNA, MessengerEZbakRGene expression regulationNonsense-mediated mRNA decayNR-seqRNA kineticsRNA quality controlSMG1iTranslation termination

Identifiers

PMID42458539

What OpenQuestion holds

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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.