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 elementsSynthaseRNASequenceEukaryotes