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 ResearchConceptsGenome activationChromatin openingTranscription factorsPioneer factor activityDifferent transcription factorsChromatin reprogrammingPioneer factorsNucleosome positionsActive enhancersIndividual genesCore histonesTriple mutantGene activationTF inputsDevelopmental transitionsSequence contextCell typesFactor activityHistonesPioneering activityEnhancerActivationSequence of eventsPou5f3Chromatin
2019
Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
Vejnar CE, Messih M, Takacs C, Yartseva V, Oikonomou P, Christiano R, Stoeckius M, Lau S, Lee M, Beaudoin JD, Musaev D, Darwich-Codore H, Walther T, Tavazoie S, Cifuentes D, Giraldez A. Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish. Genome Research 2019, 29: 1100-1114. PMID: 31227602, PMCID: PMC6633259, DOI: 10.1101/gr.245159.118.Peer-Reviewed Original ResearchConceptsAU-rich elementsMRNA stabilityZygotic transitionRich motifGenome-wide analysisRNA-protein interactionsGenome activationParallel reporterCombinatorial regulationMaternal transcriptsMiR-430Destabilizing motifsRegulatory motifsWide analysisMRNA deadenylationPosttranscriptional regulationRegulatory sequencesMost transcriptsMultiple decay pathwaysUTR sequencesSequence elementsGene expressionTarget sequenceDecay pathwaysMotifBrd4 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
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