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
Upstream ORFs are prevalent translational repressors in vertebrates
Johnstone TG, Bazzini AA, Giraldez AJ. Upstream ORFs are prevalent translational repressors in vertebrates. The EMBO Journal 2016, 35: 706-723. PMID: 26896445, PMCID: PMC4818764, DOI: 10.15252/embj.201592759.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsOpen Reading FramesProtein BiosynthesisRepressor ProteinsTranscription, GeneticVertebratesConceptsUpstream open reading framesUntranslated mRNA regionsPost-transcriptional regulationOpen reading frameMRNA leader sequenceClear repressionVertebrate transcriptomesRibosome footprintingCellular diversityTranslational repressorIndividual genesNatural selectionUpstream ORFsReading frameLeader sequenceRegulatory potentialActive translationRegulatory codeInitiation contextGene expressionMRNA regionsUnknown functionReporter experimentsVertebratesIntercistronic distance
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