2022
Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq
Biancon G, Busarello E, Joshi P, Lesch B, Halene S, Tebaldi T. Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq. STAR Protocols 2022, 3: 101823. PMID: 36595959, PMCID: PMC9676202, DOI: 10.1016/j.xpro.2022.101823.Peer-Reviewed Original ResearchConceptsProtein-RNA interactionsIndividual RNA-binding proteinsTranscriptome-wide analysisThousands of RNAsProtein-RNA contactsRNA-binding proteinSingle nucleotide levelComputational analysis pipelineRNA processingMulticomponent complexesRNA immunoprecipitationRead countsComplete detailsAnalysis pipelineAdditional levelProteinImmunoprecipitationRNAInteractionComplexes
2014
p53-directed translational control can shape and expand the universe of p53 target genes
Zaccara S, Tebaldi T, Pederiva C, Ciribilli Y, Bisio A, Inga A. p53-directed translational control can shape and expand the universe of p53 target genes. Cell Death & Differentiation 2014, 21: 1522-1534. PMID: 24926617, PMCID: PMC4158691, DOI: 10.1038/cdd.2014.79.Peer-Reviewed Original ResearchMeSH KeywordsApoptosisCell CycleCell Line, TumorDEAD-box RNA HelicasesDNADNA-Binding ProteinsDoxorubicinGene Expression ProfilingGene Expression RegulationGene Regulatory NetworksHeterogeneous Nuclear Ribonucleoprotein D0Heterogeneous-Nuclear Ribonucleoprotein DHumansImidazolesMCF-7 CellsNuclear ProteinsPeptide Chain Elongation, TranslationalPiperazinesRNARNA InterferenceRNA, MessengerRNA, Small InterferingRNA-Binding ProteinsSerine-Arginine Splicing FactorsTumor Suppressor Protein p53Y-Box-Binding Protein 1ConceptsPost-transcriptional controlTranslational controlP53-dependent cellular responseTranslational levelGenome-wide transcriptome analysisCellular responsesRNA-binding proteinCell cycle functionP53-regulated genesGene expression responsesP53 target genesP53 transcriptional targetsDirect p53 transcriptional targetP53-dependent mannerTranscription variationTranscriptional networksPolysomal profilingRNA metabolismTranslatome analysisTranscriptome analysisCellular contextTranscriptional targetsExpression responsesMaster regulatorTarget genes