Evidence map›Paper›PMID 27001511›Full record

ArticleNucleic acids research2016

Nonsense-mediated decay regulates key components of homologous recombination.

Ryan Janke, Jeremy Kong, Hannes Braberg, Greg Cantin, John R Yates, Nevan J Krogan, Wolf-Dietrich Heyer

Open access · goldAbstract read
In one paragraph

Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
0.9field-weighted citation impact, top 24% of its field
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

10 citing papers in PubMed, 20 citations in OpenAlex.

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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

7 authors at 4 institutions in 1 country.

Ryan JankeDepartment of Microbiology & Molecular Genetics, University of California, Davis, CA 95616-8665, USA.
Jeremy KongDepartment of Microbiology & Molecular Genetics, University of California, Davis, CA 95616-8665, USA.
Hannes BrabergDepartment of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2517, USA.
Greg CantinDepartment of Cell Biology, SR-11, Scripps Research institute, La Jolla, CA 92307, USA.
John R YatesDepartment of Cell Biology, SR-11, Scripps Research institute, La Jolla, CA 92307, USA.
Nevan J KroganDepartment of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2517, USA California Institute for Quantitative Biosciences, QB3, San Francisco, CA 94158-2517, USA J. David Gladstone Institute, San Francisco, CA, 94158-2517, USA.
Wolf-Dietrich HeyerDepartment of Microbiology & Molecular Genetics, University of California, Davis, CA 95616-8665, USA Department of Molecular & Cellular Biology University of California, Davis, CA 95616-8665, USA wdheyer@ucdavis.edu.
University of California, Davis · USScripps Research Institute · USGladstone Institutes · USUniversity of California, San Francisco · US

Funding

TrainingP41GM103533 · NIGMS · UNIVERSITY OF WASHINGTON · PI MACCOSS, MICHAEL · 2012 to 2021
$20.7M
Rewiring Therapeutic Cells: User-Controlled T Cells and Stem CellsP50GM081879 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LIM, WENDELL A · 2010 to 2017
$19.0M
STRUCTURAL BIOLOGY TRAINING PROGRAMT32GM008284 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KORTEMME, TANJA · 1988 to 2022
$10.1M
ENVIRONMENTAL TOXICOLOGYT32ES007059 · NIEHS · UNIVERSITY OF CALIFORNIA DAVIS · PI Laura S Van Winkle · 1985 to 2026
$7.9M
Quantitative Proteome Analysis of Brain DevelopmentR01MH067880 · NIMH · SCRIPPS RESEARCH INSTITUTE, THE · PI YATES III, JOHN R · 2003 to 2017
$7.1M
Regulation of Recombinational DNA RepairR01CA092276 · NCI · UNIVERSITY OF CALIFORNIA DAVIS · PI HEYER, WOLF-DIETRICH · 2001 to 2020
$5.2M
Comparative Analysis of Genetic Interaction NetworksR01GM084279 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI IDEKER, TREY, KROGAN, NEVAN J · 2008 to 2017
$3.9M
Genetic Analysis of the Nucleosome and RNA Polymerase II: A Systems ApproachR01GM084448 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KROGAN, NEVAN J · 2008 to 2012
$2.3M
Integrating computation and genetics to quantify specificity in protein networksR01GM098101 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KORTEMME, TANJA, KROGAN, NEVAN J · 2011 to 2014
$1.7M
NCI NIH HHS R01 CA092276NIEHS NIH HHS T32 ES007059NIGMS NIH HHS P41 GM103533NIGMS NIH HHS P50 GM081879NIGMS NIH HHS R01 GM084279NIGMS NIH HHS R01 GM084448NIGMS NIH HHS R01 GM098101NIGMS NIH HHS T32 GM008284NIMH NIH HHS R01 MH067880
6 · The paper itself

Abstract

Cells frequently experience DNA damage that requires repair by homologous recombination (HR). Proteins involved in HR are carefully coordinated to ensure proper and efficient repair without interfering with normal cellular processes. In Saccharomyces cerevisiae, Rad55 functions in the early steps of HR and is regulated in response to DNA damage through phosphorylation by the Mec1 and Rad53 kinases of the DNA damage response. To further identify regulatory processes that target HR, we performed a high-throughput genetic interaction screen with RAD55 phosphorylation site mutants. Genes involved in the mRNA quality control process, nonsense-mediated decay (NMD), were found to genetically interact with rad55 phospho-site mutants. Further characterization revealed that RAD55 transcript and protein levels are regulated by NMD. Regulation of HR by NMD extends to multiple targets beyond RAD55, including RAD51, RAD54 and RAD57 Finally, we demonstrate that loss of NMD results in an increase in recombination rates and resistance to the DNA damaging agent methyl methanesulfonate, suggesting this pathway negatively regulates HR under normal growth conditions.

Indexed as

Homologous RecombinationNonsense Mediated mRNA DecayCluster AnalysisComputational BiologyDNA-Binding ProteinsDNA DamageEpistasis, GeneticGene Expression Regulation, FungalMutationPhosphorylationSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSignal TransductionTranscription, GeneticDNA-Binding ProteinsRAD55 protein, S cerevisiaeSaccharomyces cerevisiae Proteins

Identifiers

PMID27001511
PMCPMC4914092
OpenAlexW2304063916

What OpenQuestion holds

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LicenceCC BY-NC
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.