2024
All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies
Oberdoeffer 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 elementsSynthaseRNASequenceEukaryotesBeyond 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
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