2024
UPF1 regulates mRNA stability by sensing poorly translated coding sequences
Musaev D, Abdelmessih M, Vejnar C, Yartseva V, Weiss L, Strayer E, Takacs C, Giraldez A. UPF1 regulates mRNA stability by sensing poorly translated coding sequences. Cell Reports 2024, 43: 114074. PMID: 38625794, PMCID: PMC11259039, DOI: 10.1016/j.celrep.2024.114074.Peer-Reviewed Original ResearchConceptsUpstream open reading framesOpen reading frameRegulate mRNA stabilityNonsense-mediated decayMRNA stabilityReading frameOpen reading frame lengthRegulate mRNA decayAU-rich elementsMicroRNA binding sitesCis-elementsTranslation initiationStop codonMRNA decayCodon optimizationUPF1Gene expressionBinding sitesCodonMRNAConvergent rolesHigher decay ratesMachine-learning analysisUTR
2016
Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition
Bazzini AA, del Viso F, Moreno‐Mateos M, Johnstone TG, Vejnar CE, Qin Y, Yao J, Khokha MK, Giraldez AJ. Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition. The EMBO Journal 2016, 35: 2087-2103. PMID: 27436874, PMCID: PMC5048347, DOI: 10.15252/embj.201694699.Peer-Reviewed Original ResearchConceptsZygotic transitionMRNA stabilityTranslation efficiencyMRNA clearanceMaternal mRNAsCodon identityCodon compositionGene expressionMaternal mRNA clearanceRegulated mRNA decayPost-transcriptional mechanismsAmino acid sequenceTranscript decayMRNA decayPolyadenylation statusAmino acid compositionCodon tripletsGenetic codeSynonymous codonsAcid sequenceCellular transitionsRegulatory informationNew transcriptionDevelopmental progressionMRNA
2014
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation
Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. The EMBO Journal 2014, 33: 981-993. PMID: 24705786, PMCID: PMC4193932, DOI: 10.1002/embj.201488411.Peer-Reviewed Original Research
2012
Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish
Bazzini AA, Lee MT, Giraldez AJ. Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish. Science 2012, 336: 233-237. PMID: 22422859, PMCID: PMC3547538, DOI: 10.1126/science.1215704.Peer-Reviewed Original ResearchConceptsMiR-430MRNA decayTranslational repressionMutant zebrafish embryosMessenger RNA decayNumber of ribosomesRibosome occupancyZebrafish developmentRibosome profilingTarget repressionRNA decayTranslation initiationZebrafish embryosTarget mRNAsRibosome densityEndogenous mRNAGene expressionPolyadenylate tailDeadenylationRepressionMRNAZebrafishRibosomesMicroRNAsRate of initiation
2008
MicroRNAs in Development and Disease
Staton A, Giraldez A. MicroRNAs in Development and Disease. 2008 DOI: 10.1002/9780470015902.a0020863.Peer-Reviewed Original Research