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
2022
Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2)
Karmakar S, Ramirez O, Paul KV, Gupta AK, Kumari V, Botti V, de los Mozos IR, Neuenkirchen N, Ross RJ, Karanicolas J, Neugebauer KM, Pillai MM. Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2). NAR Cancer 2022, 4: zcac015. PMID: 35528200, PMCID: PMC9070473, DOI: 10.1093/narcan/zcac015.Peer-Reviewed Original ResearchRNA binding proteinMusashi-2Functional targetIntegrative genome-wide analysisGenome-wide analysisIndividual-nucleotide resolutionAsymmetric cell divisionCell fate decisionsThousands of mRNAsKey downstream regulatorProtein Musashi-2Polysome profilingFate decisionsEukaryotic translation initiation factor 3aNucleotide resolutionCell divisionDirect RNATranslational inductionCancer stem cellsDownstream regulatorsUntranslated regionIndirect targetsBinding proteinDirect targetMere binding
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