2024
Author Correction: All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies
Oberdoerffer S, Gilbert W. Author Correction: All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies. Nature Reviews Molecular Cell Biology 2024, 1-1. PMID: 39533117, DOI: 10.1038/s41580-024-00810-3.Peer-Reviewed Original ResearchAll the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies
Oberdoerffer S, Gilbert W. All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies. Nature Reviews Molecular Cell Biology 2024, 1-12. PMID: 39433914, DOI: 10.1038/s41580-024-00784-2.Peer-Reviewed Original ResearchRNA modificationsRNA-modifying enzymesTranscriptome-wide mappingRNA modification mappingPost-transcriptional controlModified sitesSequencing depthRNA functionRNA targetsModification mappingRNAModification studiesProfiling studiesEnzymeModification sequenceNeurodevelopmental disordersTechnical artifactsFalse negativesSitesSequenceHuman healthFalse positivesTransparent reportingRluA is the major mRNA pseudouridine synthase in Escherichia coli
Schaening-Burgos C, LeBlanc H, Fagre C, Li G, Gilbert W. RluA is the major mRNA pseudouridine synthase in Escherichia coli. PLOS Genetics 2024, 20: e1011100. PMID: 39241085, PMCID: PMC11421799, DOI: 10.1371/journal.pgen.1011100.Peer-Reviewed Original ResearchConceptsPseudouridine synthasesHigh-confidence sitesMRNA-modifying enzymesE. coli mRNAsStructure probing dataIdentified target sitesTarget siteDiverse eukaryotesBacterial mRNAsRNA modificationsRluAEscherichia coliSecondary structureE. coliTRNAPseudouridineRRNAStructural motifsMRNAModification capacityRecognition elementsSynthaseRNASequenceEukaryotesRecent developments, opportunities, and challenges in the study of mRNA pseudouridylation
Gilbert W. Recent developments, opportunities, and challenges in the study of mRNA pseudouridylation. RNA 2024, 30: rna.079975.124. PMID: 38531650, PMCID: PMC11019745, DOI: 10.1261/rna.079975.124.Peer-Reviewed Original ResearchBeyond reader proteins: RNA binding proteins and RNA modifications in conversation to regulate gene expression
Fagre C, Gilbert W. Beyond reader proteins: RNA binding proteins and RNA modifications in conversation to regulate gene expression. Wiley Interdisciplinary Reviews - RNA 2024, 15: e1834. PMID: 38444048, DOI: 10.1002/wrna.1834.Peer-Reviewed Original ResearchConceptsRNA-binding proteinsRNA modificationsMRNA modificationRNA structureRNA interactionsRNA Processing > RNA EditingRNA-binding protein's bindingEffects of RNA modificationsBinding proteinGene expressionRNA-protein interactomePost-transcriptional mRNA modificationDihydrouridine (DRegulate gene expressionRNA substratesProtein-RNARNA editingRNA functionReader proteinsModification statusN1-methyladenosineCellular machinerySequence contextSecondary structureBiochemical properties
2020
Regulation and Function of RNA Pseudouridylation in Human Cells
Borchardt EK, Martinez NM, Gilbert WV. Regulation and Function of RNA Pseudouridylation in Human Cells. Annual Review Of Genetics 2020, 54: 1-28. PMID: 32870730, PMCID: PMC8007080, DOI: 10.1146/annurev-genet-112618-043830.Peer-Reviewed Original ResearchConceptsRNA pseudouridylationHuman cellsRNA-binding proteinDistinct RNA sequencesMRNA pseudouridylationPseudouridine synthasesMolecular functionsRNA metabolismPseudouridylationGene expressionRNA conformationRNA targetsProtein productionRNA sequencesMessenger RNADiverse classRNATherapeutic mRNAWidespread effectsDestabilizing interactionsCellsRecent advancesSplicingSynthasesPotential effects
2019
mRNA structure determines modification by pseudouridine synthase 1
Carlile TM, Martinez NM, Schaening C, Su A, Bell TA, Zinshteyn B, Gilbert WV. mRNA structure determines modification by pseudouridine synthase 1. Nature Chemical Biology 2019, 15: 966-974. PMID: 31477916, PMCID: PMC6764900, DOI: 10.1038/s41589-019-0353-z.Peer-Reviewed Original ResearchConceptsMRNA target recognitionMRNA pseudouridylationMRNA targetsPost-transcriptional RNA modificationsRational mutational analysisRNA-protein interactionsPseudouridine synthase 1High-throughput kinetic analysisRNA structural motifsPseudouridine synthasePseudouridine synthasesRNA pseudouridylationRNA modificationsPseudouridylationMRNA structureRNA-RNAMutational analysisGene expressionRNA structurePredominant mRNAStructural context informationSynthase 1Specific sequencesComputational predictionsStructural motifs
2018
Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast
Wang YJ, Vaidyanathan PP, Rojas-Duran MF, Udeshi ND, Bartoli KM, Carr SA, Gilbert WV. Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast. PLOS Biology 2018, 16: e2005903. PMID: 30208026, PMCID: PMC6135351, DOI: 10.1371/journal.pbio.2005903.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCodon, InitiatorConserved SequenceGene Expression Regulation, FungalHeLa CellsHumansPeptide Chain Elongation, TranslationalPeptide Chain Termination, TranslationalProtein BiosynthesisRibosomal ProteinsRibosomesRNA, RibosomalRNA, TransferSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsConceptsRibosome-binding proteinsRibosome-associated proteinsCodon-specific changesCoiled-coil domainQuantitative mass spectrometryGTPase activation centerRibosome-binding activityMost tRNAsRibosome profilingGene regulationMost genesCellular homeostasisTranslation defectsRibosomal RNATranslational recoveryComplete complementStart codonStop codonLso2Protein synthesisOpen reading frame 2ProteinImportant functionsCodonYeast
2017
Translation initiation factor eIF4G1 preferentially binds yeast transcript leaders containing conserved oligo-uridine motifs
Zinshteyn B, Rojas-Duran MF, Gilbert WV. Translation initiation factor eIF4G1 preferentially binds yeast transcript leaders containing conserved oligo-uridine motifs. RNA 2017, 23: 1365-1375. PMID: 28546148, PMCID: PMC5558906, DOI: 10.1261/rna.062059.117.Peer-Reviewed Original ResearchConceptsTranscript leaderEIF4GTranslational controlInitiation factorsRNA sequencesSpecific mRNAsEukaryotic initiation factor 4GRNA-binding preferencesGeneral initiation factorsIntrinsic sequence preferencesImportant cellular functionsCellular stress responseTranslation initiation factorTranslation of mRNAsOrganismal developmentYeast genesRibosome profilingContext-dependent differencesTranslational regulationCellular functionsPreferential translationYeast speciesKey mRNAsGene expressionSequence preference
2016
Messenger RNA modifications: Form, distribution, and function
Gilbert WV, Bell TA, Schaening C. Messenger RNA modifications: Form, distribution, and function. Science 2016, 352: 1408-1412. PMID: 27313037, PMCID: PMC5094196, DOI: 10.1126/science.aad8711.Peer-Reviewed Original ResearchConceptsStable noncoding RNAsMRNA target siteOrganismal phenotypesDevelopmental regulatorsNoncoding RNAsMRNA modificationMolecular consequencesMessenger RNAMolecular effectsRNATarget siteRecent technical advancesDistinct modificationsSparse modificationEpitranscriptomeSplicingMethyladenosineRegulatorSpeciesTechnical advancesModificationPhenotypeRegulationFunctionCells
2014
Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells
Carlile TM, Rojas-Duran MF, Zinshteyn B, Shin H, Bartoli KM, Gilbert WV. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 2014, 515: 143-146. PMID: 25192136, PMCID: PMC4224642, DOI: 10.1038/nature13802.Peer-Reviewed Original Research