2017
Dynamic 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
2012
Splicing Factor ChIP and ChRIP: Detection of Splicing and Splicing Factors at Genes by Chromatin Immunoprecipitation
Sapra A, Oesterreich F, Pabis M, Listerman I, Bardehle N, Neugebauer K. Splicing Factor ChIP and ChRIP: Detection of Splicing and Splicing Factors at Genes by Chromatin Immunoprecipitation. 2012, 416-427. DOI: 10.1002/9783527636778.ch39.Peer-Reviewed Original ResearchNascent RNASplicing factorsChromatin immunoprecipitationRNA processing intermediatesMammalian tissue culture cellsRNA processing factorsRNA polymerase IIRNA processing eventsGene of interestTissue culture cellsPolymerase IIActive histoneMRNA processingIsolation of RNAProcessing factorsProcessing eventsRNA immunoprecipitationChromatinNucleic acid complexesQuantitative RT-PCRLiving cellsProcessing intermediatesRNACulture cellsImmunoprecipitation