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
2018
Analyses of mRNA structure dynamics identify embryonic gene regulatory programs
Beaudoin JD, Novoa EM, Vejnar CE, Yartseva V, Takacs CM, Kellis M, Giraldez AJ. Analyses of mRNA structure dynamics identify embryonic gene regulatory programs. Nature Structural & Molecular Biology 2018, 25: 677-686. PMID: 30061596, PMCID: PMC6690192, DOI: 10.1038/s41594-018-0091-z.Peer-Reviewed Original ResearchConceptsGene regulatory programsUntranslated regionRegulatory programsKey maternal factorsZygotic transitionZebrafish developmentGene functionRNA functionRegulatory elementsGene expressionRNA structureRNA foldingBiological transitionsStructure dynamicsCentral roleCrucial roleCellular systemsRemodelersTranscriptomeRibosomesVivoGenesFoldingCCNA1Role
2016
RESA identifies mRNA-regulatory sequences at high resolution
Yartseva V, Takacs CM, Vejnar CE, Lee MT, Giraldez AJ. RESA identifies mRNA-regulatory sequences at high resolution. Nature Methods 2016, 14: 201-207. PMID: 28024160, PMCID: PMC5423094, DOI: 10.1038/nmeth.4121.Peer-Reviewed Original ResearchCodon 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
2006
Zebrafish MiR-430 Promotes Deadenylation and Clearance of Maternal mRNAs
Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K, Enright AJ, Schier AF. Zebrafish MiR-430 Promotes Deadenylation and Clearance of Maternal mRNAs. Science 2006, 312: 75-79. PMID: 16484454, DOI: 10.1126/science.1122689.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsAdenosineAnimalsEmbryo, NonmammalianEmbryonic DevelopmentFemaleGene Expression ProfilingGene Expression Regulation, DevelopmentalGenes, ReporterGreen Fluorescent ProteinsMicroRNAsMutationOligonucleotide Array Sequence AnalysisPolymersProtein BiosynthesisRibonuclease IIIRNA StabilityRNA, MessengerTranscription, GeneticUp-RegulationZebrafishZygoteConceptsMessenger RNA moleculesTarget messenger RNA moleculesMiR-430Vivo target validationVertebrate genesZygotic transcriptionEarly embryogenesisRNA moleculesMicroarray approachVivo functionDeadenylationTarget validationEarly developmentMechanism of actionMost targetsEmbryogenesisMorphogenesisTranscriptionGenesMicroRNAsTarget