2022
The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation
Miao L, Tang Y, Bonneau AR, Chan SH, Kojima ML, Pownall ME, Vejnar CE, Gao F, Krishnaswamy S, Hendry CE, Giraldez AJ. The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation. Molecular Cell 2022, 82: 986-1002.e9. PMID: 35182480, PMCID: PMC9327391, DOI: 10.1016/j.molcel.2022.01.024.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChromatinGenomeHistonesNucleosomesSOX Transcription FactorsZebrafishZebrafish ProteinsConceptsGenome activationChromatin openingTranscription factorsPioneer factor activityDifferent transcription factorsChromatin reprogrammingPioneer factorsNucleosome positionsActive enhancersIndividual genesCore histonesTriple mutantGene activationTF inputsDevelopmental transitionsSequence contextCell typesFactor activityHistonesPioneering activityEnhancerActivationSequence of eventsPou5f3Chromatin
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
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
2013
Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition
Lee MT, Bonneau AR, Takacs CM, Bazzini AA, DiVito KR, Fleming ES, Giraldez AJ. Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition. Nature 2013, 503: 360-364. PMID: 24056933, PMCID: PMC3925760, DOI: 10.1038/nature12632.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCellular ReprogrammingEmbryonic DevelopmentFemaleGene Expression ProfilingGene Expression Regulation, DevelopmentalHomeodomain ProteinsMicroRNAsMothersNanog Homeobox ProteinOctamer Transcription Factor-3Pluripotent Stem CellsRibosomesSOXB1 Transcription FactorsTranscriptomeZebrafishZebrafish ProteinsZygoteConceptsZygotic genome activationZygotic transitionMiR-430Zygotic gene expressionZygotic gene activationZygotic developmental programMaternal messenger RNAsZygotic programGenome activationZygotic genesZygotic transcriptionRibosome profilingDevelopmental programGene activationTranscription factorsDevelopmental arrestGene expressionSoxB1POU5F1Maternal programMessenger RNANanogGastrulationZebrafishGenes
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