Featured Publications
STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts
Zimmer JT, Rosa-Mercado NA, Canzio D, Steitz JA, Simon MD. STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts. Molecular Cell 2021, 81: 4398-4412.e7. PMID: 34520723, PMCID: PMC9020433, DOI: 10.1016/j.molcel.2021.08.019.Peer-Reviewed Original ResearchConceptsPause releaseRNA polymerase II transcriptsRNA polymerase II moleculesCis-acting DNA elementsTATA box-containing promotersPolymerase II transcriptsPromoter-proximal pausingCritical regulatory functionsTranscriptional regulationRNA turnoverTranscriptional controlDNA elementsTranscriptional shutdownPause sitesHyperosmotic stressRegulatory mechanismsRegulatory functionsPrinciples of regulationHormonal stimuliPausingPremature terminationTranscriptsRegulationAcetyl-methyllysine marks chromatin at active transcription start sites
Lu-Culligan W, Connor L, Xie Y, Ekundayo B, Rose B, Machyna M, Pintado-Urbanc A, Zimmer J, Vock I, Bhanu N, King M, Garcia B, Bleichert F, Simon M. Acetyl-methyllysine marks chromatin at active transcription start sites. Nature 2023, 622: 173-179. PMID: 37731000, PMCID: PMC10845139, DOI: 10.1038/s41586-023-06565-9.Peer-Reviewed Original ResearchConceptsPost-translational modificationsLysine residuesActive transcription start sitesTranscription start siteRange of speciesChromatin biologyChromatin proteinsLysine methylationActive chromatinProteins BRD2Transcriptional initiationLysine acetylationHistone H4Start siteMammalian tissuesHuman diseasesSame residuesMethylationAcetylationChromatinResiduesProteinBiological signalsHistonesBRD2Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin
Machyna M, Kiefer L, Simon MD. Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin. Nature Structural & Molecular Biology 2020, 27: 297-304. PMID: 32157249, DOI: 10.1038/s41594-020-0390-z.Peer-Reviewed Original ResearchConceptsHybridization capture approachGenome-wide changesLong non-coding RNAsUnfolded protein responseNon-coding RNAsStrand exchange reactionLncRNA localizationIndividual RNAsRNA captureUncharacterized changesX chromosomeProtein responseHeat shockChromatinLncRNAsRNACapture approachBinding sitesNucleic acidsNucleotide chemistryRoX2AutosomesChromosomesRelocalizationSpeciesTimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding
Schofield JA, Duffy EE, Kiefer L, Sullivan MC, Simon MD. TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding. Nature Methods 2018, 15: 221-225. PMID: 29355846, PMCID: PMC5831505, DOI: 10.1038/nmeth.4582.Peer-Reviewed Original ResearchHigh-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation
Simon MD, Pinter SF, Fang R, Sarma K, Rutenberg-Schoenberg M, Bowman SK, Kesner BA, Maier VK, Kingston RE, Lee JT. High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation. Nature 2013, 504: 465-469. PMID: 24162848, PMCID: PMC3904790, DOI: 10.1038/nature12719.Peer-Reviewed Original Research
2024
Disulfide Tethering to Map Small Molecule Binding Sites Transcriptome-wide
Moon M, Vock I, Streit A, Connor L, Senkina J, Ellman J, Simon M. Disulfide Tethering to Map Small Molecule Binding Sites Transcriptome-wide. ACS Chemical Biology 2024, 19: 2081-2086. PMID: 39192734, DOI: 10.1021/acschembio.4c00538.Peer-Reviewed Original ResearchCytochrome c oxidase 1Binding sitesRNA-small molecule interactionsPotential binding sitesTranscriptome-wide screeningSmall molecule disulfideSpinal muscular atrophyCellular RNARNA sitesTarget RNAMetabolic labelingSmall molecule bindingRNADisulfide analoguesLead moleculesMolecule bindingTranscriptomeFDA-approved drugsStructural probesMolecule interactionsCovalent attachmentDisulfide tetherThermodynamic propertiesTreat spinal muscular atrophyDisulfidePhosphorylation of the nuclear poly(A) binding protein (PABPN1) during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics
Gordon J, Phizicky D, Schärfen L, Brown C, Escayola D, Kanyo J, Lam T, Simon M, Neugebauer K. Phosphorylation of the nuclear poly(A) binding protein (PABPN1) during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics. Nucleic Acids Research 2024, 52: 9886-9903. PMID: 38943343, PMCID: PMC11381358, DOI: 10.1093/nar/gkae562.Peer-Reviewed Original ResearchPoly(A)-binding proteinTranscriptome dynamicsNuclear poly(A) binding proteinPoly(A) binding proteinMode of gene regulationFunctional consequences of phosphorylationLong-read sequencingIncreased mRNA turnoverNucleo-cytoplasmic exportConsequences of phosphorylationRegulation of poly(ACohort of mRNAsGene expression programsMRNA biogenesisCytoplasmic mixingMRNA turnoverGene regulationShorter poly(ARNA stabilityMitotic kinasesPoly(ACell cycleMRNA synthesisIncreased transcriptionBinding proteinTranscription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape
Boddu P, Gupta A, Roy R, De La Peña Avalos B, Olazabal-Herrero A, Neuenkirchen N, Zimmer J, Chandhok N, King D, Nannya Y, Ogawa S, Lin H, Simon M, Dray E, Kupfer G, Verma A, Neugebauer K, Pillai M. Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape. Molecular Cell 2024, 84: 1475-1495.e18. PMID: 38521065, PMCID: PMC11061666, DOI: 10.1016/j.molcel.2024.02.032.Peer-Reviewed Original ResearchRate of RNA polymerase IIChromatin landscapeElongation defectsElongation rate of RNA polymerase IIImpaired protein-protein interactionsSplicing of pre-messenger RNATranscription elongation defectsRNA polymerase IIProtein-protein interactionsPre-messenger RNACancer-associated mutationsIsogenic cell linesSin3/HDAC complexGene bodiesPolymerase IIChromatin accessibilityH3K4me3 markChromatin changesMutant SF3B1ChromatinMutant mouse modelsEpigenetic disordersEpigenetic factorsHuman diseasesMutant state
2023
Impaired Early Spliceosome Complex Assembly Underlies Gene Body Elongation Transcription Defect in SF3B1K700E
Boddu P, Gupta A, Roy R, De La Pena Avalos B, Herrero A, Zimmer J, Simon M, Chandhok N, King D, Neuenkirchen N, Dray E, Lin H, Kupfer G, Verma A, Neugebauer K, Pillai M. Impaired Early Spliceosome Complex Assembly Underlies Gene Body Elongation Transcription Defect in SF3B1K700E. Blood 2023, 142: 714. DOI: 10.1182/blood-2023-187303.Peer-Reviewed Original ResearchSplicing factorsChIP-seqK562 cell lineKey regulatory genesCell linesSingle mutant alleleNon-denaturing gelsAlternative splicingTranscriptional kineticsRegulatory genesSpliceosome assemblySplicing efficiencyMRNA splicingCRISPR/Progenitor populationsNeomorphic functionsMolecular mechanismsMutant allelesIsoform changesGene editingNovel mechanismMutationsSF mutationsRecurrent mutationsAssembly kineticsALKBH5 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-KGCatalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
Abini-Agbomson S, Gretarsson K, Shih R, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon M, Armache J, Nudler E, Narlikar G, Liu S, Lu C, Armache K. Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. Molecular Cell 2023, 83: 2872-2883.e7. PMID: 37595555, DOI: 10.1016/j.molcel.2023.07.020.Peer-Reviewed Original ResearchConceptsNon-catalytic activitiesNon-catalytic mechanismHistone H4 lysine 20Histone variant H2A.ZH4 lysine 20Large macromolecular complexesCatalytic activityHeterochromatin formationHeterochromatin functionVariant H2A.ZLysine 20Nucleosome substratesGenomic stabilityDNA replicationNucleosomal DNAHistone methyltransferaseChromatin condensationSUV420H1Histone octamerMacromolecular complexesCryoelectron microscopyCellular analysisEssential roleDistinct phenotypesCrucial roleSystematic 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 variationDDX5RibosomesMCM2RNAAbundanceRegulationTargeted Degradation of mRNA Decapping Enzyme DcpS by a VHL-Recruiting PROTAC
Swartzel JC, Bond MJ, Pintado-Urbanc AP, Daftary M, Krone MW, Douglas T, Carder EJ, Zimmer JT, Maeda T, Simon MD, Crews CM. Targeted Degradation of mRNA Decapping Enzyme DcpS by a VHL-Recruiting PROTAC. ACS Chemical Biology 2022, 17: 1789-1798. PMID: 35749470, PMCID: PMC10367122, DOI: 10.1021/acschembio.2c00145.Peer-Reviewed Original ResearchFunctional elements of the cis-regulatory lincRNA-p21
Winkler L, Jimenez M, Zimmer JT, Williams A, Simon MD, Dimitrova N. Functional elements of the cis-regulatory lincRNA-p21. Cell Reports 2022, 39: 110687. PMID: 35443176, PMCID: PMC9118141, DOI: 10.1016/j.celrep.2022.110687.Peer-Reviewed Original ResearchConceptsGene expression controlFull-length transcriptionDNA regulatory elementsCell cycle genesCDKN1A/p21P53-dependent expressionFunctional elementsChromatin organizationLncRNA lociNascent transcriptionRegulatory lociExpression controlCycle genesLncRNA transcriptsRegulatory elementsMolecular mechanismsTranscriptionExon 1LincRNA-p21LociP21 expressionGenetic modelsAccumulationExpressionSplicingPrecision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies
Biancon G, Joshi P, Zimmer JT, Hunck T, Gao Y, Lessard MD, Courchaine E, Barentine AES, Machyna M, Botti V, Qin A, Gbyli R, Patel A, Song Y, Kiefer L, Viero G, Neuenkirchen N, Lin H, Bewersdorf J, Simon MD, Neugebauer KM, Tebaldi T, Halene S. Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. Molecular Cell 2022, 82: 1107-1122.e7. PMID: 35303483, PMCID: PMC8988922, DOI: 10.1016/j.molcel.2022.02.025.Peer-Reviewed Original Research
2021
Noncoding RNAs: biology and applications—a Keystone Symposia report
Cable J, Heard E, Hirose T, Prasanth KV, Chen L, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen C, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Noncoding RNAs: biology and applications—a Keystone Symposia report. Annals Of The New York Academy Of Sciences 2021, 1506: 118-141. PMID: 34791665, PMCID: PMC9808899, DOI: 10.1111/nyas.14713.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsKeystone Symposia reportPotential drug targetsRNA biologyHuman transcriptomeEpigenetic modificationsKeystone eSymposiumNoncoding RNAsCell signalingBasic biologyDrug targetsRNABiologyDisease mechanismsNucleotidesSpeciesTranscriptomeImportant roleRNAsTranscriptionSymposium reportSignalingTranslationRoleTargetHyperosmotic 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
2020
Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitor
Luo Y, Schofield JA, Na Z, Hann T, Simon MD, Slavoff SA. Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitor. Cell Chemical Biology 2020, 28: 463-474.e7. PMID: 33357462, PMCID: PMC8052284, DOI: 10.1016/j.chembiol.2020.12.003.Peer-Reviewed Original ResearchConceptsRNA decayEnzyme DCP2P-bodiesDCP2Genetic approachesRNA substratesBicyclic peptide inhibitorsHuman RNAExpression changesCellular substratesPhage display selectionSelective chemical inhibitorsChemical inhibitorsHuman cellsGenetic ablationBicyclic peptide ligandsPeptide inhibitorCP21Display selectionPeptide ligandsHigh affinityRegulomeTranscriptionInhibitorsPowerful tool