2024
NaP-TRAP reveals the regulatory grammar in 5’UTR-mediated translation regulation during zebrafish development
Strayer E, Krishna S, Lee H, Vejnar C, Neuenkirchen N, Gupta A, Beaudoin J, Giraldez A. NaP-TRAP reveals the regulatory grammar in 5’UTR-mediated translation regulation during zebrafish development. Nature Communications 2024, 15: 10898. PMID: 39738051, PMCID: PMC11685710, DOI: 10.1038/s41467-024-55274-y.Peer-Reviewed Original ResearchConceptsMassively parallel reporter assaysCis-regulatory elementsMaternal-to-zygotic transitionGC-rich motifsU-rich motifsTrans-acting proteinsRepressor of translationRibosome affinity purificationRegulatory grammarUpstream ORFsZygotic expressionTranslational switchReporter mRNATranslational controlTranslational regulationNascent peptideAffinity purificationMicroRNA sitesPolysome profilingMRNA translationZebrafish developmentMRNA stabilityExpression of miR-430MiR-430Regulatory functions
2019
Brd4 and P300 Confer Transcriptional Competency during Zygotic Genome Activation
Chan SH, Tang Y, Miao L, Darwich-Codore H, Vejnar CE, Beaudoin JD, Musaev D, Fernandez JP, Benitez MDJ, Bazzini AA, Moreno-Mateos MA, Giraldez AJ. Brd4 and P300 Confer Transcriptional Competency during Zygotic Genome Activation. Developmental Cell 2019, 49: 867-881.e8. PMID: 31211993, PMCID: PMC7201981, DOI: 10.1016/j.devcel.2019.05.037.Peer-Reviewed Original ResearchConceptsGenome activationTranscriptional competencyHistone acetylationP300-dependent histone acetylationZygotic genome activationFirst zygotic genesMaternal mRNA translationZygotic genesAnimal developmentZygotic developmentDevelopmental reprogrammingMRNA translationLive imagingCell cycleSilent genomeBRD4ZebrafishGenomeTranscriptionAcetylationActivationP300FertilizationReprogrammingGenes
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 Research
2015
CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo
Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nature Methods 2015, 12: 982-988. PMID: 26322839, PMCID: PMC4589495, DOI: 10.1038/nmeth.3543.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
2010
A Novel miRNA Processing Pathway Independent of Dicer Requires Argonaute2 Catalytic Activity
Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson ND, Wolfe SA, Giraldez AJ. A Novel miRNA Processing Pathway Independent of Dicer Requires Argonaute2 Catalytic Activity. Science 2010, 328: 1694-1698. PMID: 20448148, PMCID: PMC3093307, DOI: 10.1126/science.1190809.Peer-Reviewed Original ResearchAnimalsArgonaute ProteinsBiocatalysisEmbryo, NonmammalianEmbryonic DevelopmentErythropoiesisEukaryotic Initiation Factor-2HumansMicroRNAsModels, BiologicalMorphogenesisNucleic Acid ConformationRecombinant ProteinsRibonuclease IIIRNA PrecursorsRNA Processing, Post-TranscriptionalZebrafishZebrafish Proteins
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
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