2023
Five questions on how biochemistry can combat climate change
Chen K, Guo Y, How K, Acosta A, Documet D, Liang C, Arul D, Wood S, Moon K, Oliver L, Fajardo E, Kopyto M, Shine M, Neugebauer K. Five questions on how biochemistry can combat climate change. BBA Advances 2023, 4: 100111. PMID: 38075469, PMCID: PMC10709155, DOI: 10.1016/j.bbadva.2023.100111.Peer-Reviewed Original ResearchClimate changeCell biologyGreater ecosystemMolecular biophysicsEnvironmental changesEnvironmental conditionsOrganismsBiochemistryMolecular pointNew diseaseHuman activitiesDispersalMicrobesGeneticsBiologyEcosystemsPlantsGlobal warmingPathwayHigh levelsSalt concentrationBiophysicsCellsAccumulationWeather patterns
2022
Transcriptome-wide mapping reveals a diverse dihydrouridine landscape including mRNA
Draycott AS, Schaening-Burgos C, Rojas-Duran MF, Wilson L, Schärfen L, Neugebauer KM, Nachtergaele S, Gilbert WV. Transcriptome-wide mapping reveals a diverse dihydrouridine landscape including mRNA. PLOS Biology 2022, 20: e3001622. PMID: 35609439, PMCID: PMC9129914, DOI: 10.1371/journal.pbio.3001622.Peer-Reviewed Original ResearchConceptsTranscriptome-wide mappingSmall nucleolar RNAsFunctional RNA structuresSingle-nucleotide resolutionStem-loop regionEukaryotic ribosomesNucleolar RNAsPre-mRNARNA structureRNA targetsDihydrouridine synthaseHuman diseasesMRNARNANovel classFunctional componentsSplicingTRNARibosomesYeastDependent changesLandscapeOrganismsDihydrouridineSequencingIdentification of Alternative Polyadenylation in Cyanidioschyzon merolae Through Long-Read Sequencing of mRNA
Schärfen L, Zigackova D, Reimer KA, Stark MR, Slat VA, Francoeur NJ, Wells ML, Zhou L, Blackshear PJ, Neugebauer KM, Rader SD. Identification of Alternative Polyadenylation in Cyanidioschyzon merolae Through Long-Read Sequencing of mRNA. Frontiers In Genetics 2022, 12: 818697. PMID: 35154260, PMCID: PMC8831791, DOI: 10.3389/fgene.2021.818697.Peer-Reviewed Original ResearchAlternative polyadenylationNon-model organismsRNA processing pathwaysLong-Read SequencingCyanidioschyzon merolaeSplicing statusSplicing machineryMammalian cellsRegulatory stepMRNA stabilityRed algaVolcanic hot springsGene expressionRich mediumPolyadenylationBiological importanceOrganismsSite usageProtein expressionHot springsYeastAlgaProcessing pathwaysSequencingMRNA
2017
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 frontierVivo
2015
Coilin: The first 25 years
Machyna M, Neugebauer KM, Staněk D. Coilin: The first 25 years. RNA Biology 2015, 12: 590-596. PMID: 25970135, PMCID: PMC4615369, DOI: 10.1080/15476286.2015.1034923.Peer-Reviewed Original Research
2013
Counting on co-transcriptional splicing
Brugiolo M, Herzel L, Neugebauer KM. Counting on co-transcriptional splicing. Faculty Reviews 2013, 5: 9. PMID: 23638305, PMCID: PMC3619158, DOI: 10.12703/p5-9.Peer-Reviewed Original ResearchCo-transcriptional splicingMultiple model organismsProcess of transcriptionModel organismsSplicing machineryTranscription terminationSplicing eventsIntron removalMammalian cellsIntron sequencesBioinformatics analysisPlace coSplicingExperimental accessibilityMost cellsGlobal datasetTranscriptionOrganismsMRNAExperimental approachBroad differencesSpliceosomeInsectsCellsYeast