2023
ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m6A modification-mediated RNA stability control
Gao Y, Zimmer J, Vasic R, Liu C, Gbyli R, Zheng S, Patel A, Liu W, Qi Z, Li Y, Nelakanti R, Song Y, Biancon G, Xiao A, Slavoff S, Kibbey R, Flavell R, Simon M, Tebaldi T, Li H, Halene S. ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m6A modification-mediated RNA stability control. Cell Reports 2023, 42: 113163. PMID: 37742191, PMCID: PMC10636609, DOI: 10.1016/j.celrep.2023.113163.Peer-Reviewed Original ResearchConceptsAlkB homolog 5Post-transcriptional regulatory mechanismsHematopoietic stemNumerous cellular processesProgenitor cell fitnessEnergy metabolismMitochondrial ATP productionMethyladenosine (m<sup>6</sup>A) RNA modificationTricarboxylic acid cycleCell energy metabolismHuman hematopoietic cellsMitochondrial energy productionCell fitnessCellular processesRNA modificationsRNA methylationRegulatory mechanismsEnzyme transcriptsATP productionHomolog 5Acid cycleΑ-ketoglutarateHematopoietic cellsMessenger RNAΑ-KGSystematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq
Patel S, Sexton A, Strine M, Wilen C, Simon M, Pyle A. Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq. Nature Communications 2023, 14: 3426. PMID: 37296103, PMCID: PMC10255950, DOI: 10.1038/s41467-023-38623-1.Peer-Reviewed Original ResearchbakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling
Vock I, Simon M. bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling. RNA 2023, 29: 958-976. PMID: 37028916, PMCID: PMC10275263, DOI: 10.1261/rna.079451.122.Peer-Reviewed Original ResearchConceptsBayesian hierarchical modelingAdvanced statistical modelsHierarchical modelingDifferential expression analysisStatistical modelBayesian analysisRNA synthesisExpression analysisStatistical rigorData setsR packageRNA sequencing dataCellular RNA levelsMethods addressStatistical powerKinetics of RNAImproved analysisSequencing dataModel outperformsUser-friendly softwareModelingSetRNA levelsModelDifferential kinetics
2022
Internally controlled RNA sequencing comparisons using nucleoside recoding chemistry
Courvan MCS, Niederer RO, Vock IW, Kiefer L, Gilbert WV, Simon MD. Internally controlled RNA sequencing comparisons using nucleoside recoding chemistry. Nucleic Acids Research 2022, 50: e110-e110. PMID: 36018791, PMCID: PMC9638901, DOI: 10.1093/nar/gkac693.Peer-Reviewed Original ResearchConceptsBiochemical manipulationRNA polymerase II inhibitionSodium arsenite stressSet of transcriptsNew biological understandingTranscript regulationArsenite stressMRNA associationRNA transcriptsBiological insightsHeat shockMetabolic labelBiological understandingRNA contentRNA levelsTranscriptsCell culturesII inhibitionBiological variationDDX5RibosomesMCM2RNAAbundanceRegulation
2021
Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression
Rosa-Mercado NA, Zimmer JT, Apostolidi M, Rinehart J, Simon MD, Steitz JA. Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression. Molecular Cell 2021, 81: 502-513.e4. PMID: 33400923, PMCID: PMC7867636, DOI: 10.1016/j.molcel.2020.12.002.Peer-Reviewed Original ResearchConceptsWidespread transcriptional repressionTranscriptional repressionPol IIIntegrator complex subunitsRNA polymerase IIGenome-wide lossStress-induced redistributionParental genesTranscriptional outputDoG inductionPolymerase IIChIP sequencingHuman cell linesUpstream geneComplex subunitsPolyadenylation factorsTranscription profilesReadthrough transcriptsCatalytic subunitIntegrator activityCellular stressHyperosmotic stressTranscriptional levelTranscription resultsGenes
2019
Reengineering a tRNA Methyltransferase To Covalently Capture New RNA Substrates
Smith TS, Zoltek MA, Simon MD. Reengineering a tRNA Methyltransferase To Covalently Capture New RNA Substrates. Journal Of The American Chemical Society 2019, 141: 17460-17465. PMID: 31626536, DOI: 10.1021/jacs.9b08529.Peer-Reviewed Original ResearchConceptsSubstrate specificityRNA substratesSubstrate RNARNA substrate specificityWild-type proteinCovalent RNA modificationsHigh-throughput sequencing assaysDouble mutantRNA modificationsTriple mutantSubstrate mutantsTRNA methyltransferaseProtein engineeringRNA transcriptsMutantsRational engineeringRNASubstrate screeningTRMASequencing assaysMethyltransferaseEnzymeProteinPowerful toolSpecificity
2018
Carbodiimide reagents for the chemical probing of RNA structure in cells
Wang PY, Sexton AN, Culligan WJ, Simon MD. Carbodiimide reagents for the chemical probing of RNA structure in cells. RNA 2018, 25: 135-146. PMID: 30389828, PMCID: PMC6298570, DOI: 10.1261/rna.067561.118.Peer-Reviewed Original ResearchConceptsConformation of RNAU nucleotidesIntact cellsChemical probesDimethyl sulfateNucleotides of RNASingle-stranded nucleotidesXist lncRNACellular contextNoncoding RNAsRNA elementsSHAPE reagentsAccessible nucleotidesRNA conformationRNA structureBiological contextChemical probingWatson-Crick faceCellular environmentFunctional roleCarbodiimide reagentRNA nucleotidesRNANucleotidesStructured regionsGaining insight into transcriptome‐wide RNA population dynamics through the chemistry of 4‐thiouridine
Duffy EE, Schofield JA, Simon MD. Gaining insight into transcriptome‐wide RNA population dynamics through the chemistry of 4‐thiouridine. Wiley Interdisciplinary Reviews - RNA 2018, 10: e1513. PMID: 30370679, PMCID: PMC6768404, DOI: 10.1002/wrna.1513.Peer-Reviewed Original ResearchConceptsDifferent RNA populationsRNA populationsNumerous experimental strategiesCellular RNA levelsMetabolic labeling experimentsRNA levelsRNA metabolismRNA turnoverRNA stabilityRNA transcriptionRNA sequencingMetabolic labelingPopulation dynamicsMetabolic labelTargeted incorporationRNA analysisRNA methodWhole cellsC mutationLabeling experimentsExperimental strategiesSequencingAvailable poolGenomeCellsExpanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6‑Thioguanosine
Kiefer L, Schofield JA, Simon MD. Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6‑Thioguanosine. Journal Of The American Chemical Society 2018, 140: 14567-14570. PMID: 30353734, PMCID: PMC6779120, DOI: 10.1021/jacs.8b08554.Peer-Reviewed Original ResearchSolid phase chemistry to covalently and reversibly capture thiolated RNA
Duffy EE, Canzio D, Maniatis T, Simon MD. Solid phase chemistry to covalently and reversibly capture thiolated RNA. Nucleic Acids Research 2018, 46: gky556-. PMID: 29986098, PMCID: PMC6101502, DOI: 10.1093/nar/gky556.Peer-Reviewed Original Research
2017
Catching RNAs on chromatin using hybridization capture methods
Machyna M, Simon MD. Catching RNAs on chromatin using hybridization capture methods. Briefings In Functional Genomics 2017, 17: 96-103. PMID: 29126220, PMCID: PMC5888980, DOI: 10.1093/bfgp/elx038.Peer-Reviewed Original ResearchConceptsRNA affinity purificationHybridization capture methodsCross-linked chromatin extractsGenome-wide scaleEnrichment of RNAInteraction of lncRNAsLncRNA localizationChromatin isolationChromatin extractsSite of interactionCapture methodAffinity purificationBiological roleRNA targetsHybridization analysisRNARNA purificationChromatinLncRNAsOligonucleotide hybridizationPurificationDevelopment of methodsProteinCapture experimentsHybridizationInterpreting Reverse Transcriptase Termination and Mutation Events for Greater Insight into the Chemical Probing of RNA
Sexton AN, Wang PY, Rutenberg-Schoenberg M, Simon MD. Interpreting Reverse Transcriptase Termination and Mutation Events for Greater Insight into the Chemical Probing of RNA. Biochemistry 2017, 56: 4713-4721. PMID: 28820243, PMCID: PMC5648349, DOI: 10.1021/acs.biochem.7b00323.Peer-Reviewed Original Research