Analysis of RNA-protein interactions in vertebrate embryos using UV crosslinking approaches
Despic V, Dejung M, Butter F, Neugebauer KM. Analysis of RNA-protein interactions in vertebrate embryos using UV crosslinking approaches. Methods 2017, 126: 44-53. PMID: 28734934, DOI: 10.1016/j.ymeth.2017.07.013.Peer-Reviewed Original ResearchConceptsNumber of RBPsRNA-protein interactionsUnique biological contextZebrafish Danio rerioRegulated gene expressionInteractome captureVertebrate embryosDanio rerioRNA-seqCellular RNAGene expressionBiological contextRBPsRNAProteinGenomeRerioCrosslinking approachOrganismsEmbryosMRNAAnnotationExpressionVast frontierVivoDynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition
Despic V, Dejung M, Gu M, Krishnan J, Zhang J, Herzel L, Straube K, Gerstein MB, Butter F, Neugebauer KM. Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition. Genome Research 2017, 27: 1184-1194. PMID: 28381614, PMCID: PMC5495070, DOI: 10.1101/gr.215954.116.Peer-Reviewed Original ResearchConceptsZygotic genome activationRNA-protein interactionsMaternal mRNAsZygotic transitionSplicing factorsDynamic RNA-protein interactionsMRNA interactome capturePost-transcriptional regulationMRNA splicing factorsRNA processing eventsTranscription-dependent mannerNumerous splicing factorsInteractome captureGenome activationSequence-specific associationHnRNP proteinsRNA metabolismDramatic translocationZebrafish embryosProcessing eventsICLIP dataDevelopmental transitionsRNA targetsReporter assaysProtein constellations