2025
QKI-induced circ_0001766 inhibits colorectal cancer progression and rapamycin resistance by miR-1203/PPP1R3C/mTOR/Myc axis
Zhou Y, Gao Y, Peng Y, Cai C, Han Y, Chen Y, Deng G, Ouyang Y, Shen H, Zeng S, Du Y, Xiao Z. QKI-induced circ_0001766 inhibits colorectal cancer progression and rapamycin resistance by miR-1203/PPP1R3C/mTOR/Myc axis. Cell Death Discovery 2025, 11: 192. PMID: 40263288, PMCID: PMC12015279, DOI: 10.1038/s41420-025-02478-w.Peer-Reviewed Original ResearchCRC cell proliferationCircular RNAsCompetitive endogenous RNAColorectal cancer tissuesInhibited CRC cell proliferationColorectal cancer progressionRapamycin resistanceColorectal cancerEndogenous RNADrug resistancePhosphorylation of MycRNA-binding proteinsModulating CRC progressionRate of drug resistanceActivation of mTOR signalingCell proliferationAssociated with patient survivalPre-mRNACircRNAsQKI expressionMYC phosphorylationIntron 1MYC pathwayCRC progressionInduce apoptosisRapid folding of nascent RNA regulates eukaryotic RNA biogenesis
Schärfen L, Vock I, Simon M, Neugebauer K. Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis. Molecular Cell 2025, 85: 1561-1574.e5. PMID: 40139190, PMCID: PMC12009195, DOI: 10.1016/j.molcel.2025.02.025.Peer-Reviewed Original ResearchConceptsRibosome biogenesisBase pairsNascent pre-mRNACo-transcriptional foldingRNA processing eventsRNA base pairsRDNA lociNascent RNARNA biogenesisRNA polymerasePol IIRRNA nucleotidesNascent chainsPol ICoding PotentialPairing statusPre-mRNAMature mRNABase-paired stateElongating ribosomeFunctional conformationProcessing eventsBiogenesisRibosomeNucleotide
2024
Emerging and re-emerging themes in co-transcriptional pre-mRNA splicing
Carrocci T, Neugebauer K. Emerging and re-emerging themes in co-transcriptional pre-mRNA splicing. Molecular Cell 2024, 84: 3656-3666. PMID: 39366353, PMCID: PMC11463726, DOI: 10.1016/j.molcel.2024.08.036.Peer-Reviewed Original ResearchConceptsPre-mRNA splicingCo-transcriptional pre-mRNA splicingCo-transcriptional RNA foldingCo-transcriptional processesRNA polymerase IIPre-messenger RNAFunctional messenger RNAsCapping enzymePolymerase IIDelayed splicingPolyadenylation machinerySplicing eventsPre-mRNAGene regulationMacromolecular machinesRNA foldingRNA synthesisMRNA isoformsProtein productionGene expressionSplicingRNARegulatory importanceCross-regulationMessenger RNANuclear PKM2 binds pre-mRNA at folded G-quadruplexes and reveals their gene regulatory role
Anastasakis D, Apostolidi M, Garman K, Polash A, Umar M, Meng Q, Scutenaire J, Jarvis J, Wang X, Haase A, Brownell I, Rinehart J, Hafner M. Nuclear PKM2 binds pre-mRNA at folded G-quadruplexes and reveals their gene regulatory role. Molecular Cell 2024, 84: 3775-3789.e6. PMID: 39153475, PMCID: PMC11455610, DOI: 10.1016/j.molcel.2024.07.025.Peer-Reviewed Original ResearchRNA-binding proteinsPre-mRNANon-canonical RNA-binding proteinsGene regulatory roleCancer cellsRNA G-quadruplexesG-quadruplexInvasion of cancer cellsTriple-negative breast cancer cellsBreast cancer cellsEpithelial-to-mesenchymal transitionCancer typesNuclear localizationPrecursor mRNANuclear accumulationGene expressionXenograft mouse modelNuclear PKM2Regulatory roleRG4sPKM2Reduced migrationMouse modelTumor progressionPatient survivalThe cytidine deaminase APOBEC3A regulates nucleolar function to promote cell growth and ribosome biogenesis
McCool M, Bryant C, Abriola L, Surovtseva Y, Baserga S. The cytidine deaminase APOBEC3A regulates nucleolar function to promote cell growth and ribosome biogenesis. PLOS Biology 2024, 22: e3002718. PMID: 38976757, PMCID: PMC11257408, DOI: 10.1371/journal.pbio.3002718.Peer-Reviewed Original ResearchRibosome biogenesis factorsRibosome biogenesisBiogenesis factorsCell growthNucleolar functionRegulation of nucleolar functionHuman ribosome biogenesisProtein synthesisProduction of ribosomesFamily of proteinsSource of mutagenesisLevel of protein synthesisCytidine deaminase familyIncreased cell growthPromote cell growthPre-rRNAPotential direct rolePre-mRNATransient overexpressionRibosomeGenomic mutationsBiogenesisMCF10A cellsMaturation stepsAPOBEC3A
2022
Transcriptome-wide mapping reveals a diverse dihydrouridine landscape including mRNA
Draycott AS, Schaening-Burgos C, Rojas-Duran MF, Wilson L, Schärfen L, Neugebauer KM, Nachtergaele S, Gilbert WV. Transcriptome-wide mapping reveals a diverse dihydrouridine landscape including mRNA. PLOS Biology 2022, 20: e3001622. PMID: 35609439, PMCID: PMC9129914, DOI: 10.1371/journal.pbio.3001622.Peer-Reviewed Original ResearchConceptsTranscriptome-wide mappingSmall nucleolar RNAsFunctional RNA structuresSingle-nucleotide resolutionStem-loop regionEukaryotic ribosomesNucleolar RNAsPre-mRNARNA structureRNA targetsDihydrouridine synthaseHuman diseasesMRNARNANovel classFunctional componentsSplicingTRNARibosomesYeastDependent changesLandscapeOrganismsDihydrouridineSequencing
2018
Architecture of the U6 snRNP reveals specific recognition of 3′-end processed U6 snRNA
Montemayor E, Didychuk A, Yake A, Sidhu G, Brow D, Butcher S. Architecture of the U6 snRNP reveals specific recognition of 3′-end processed U6 snRNA. Nature Communications 2018, 9: 1749. PMID: 29717126, PMCID: PMC5931518, DOI: 10.1038/s41467-018-04145-4.Peer-Reviewed Original ResearchConceptsU6 small nuclear RNASmall nuclear RNAPre-mRNAU6 snRNPPre-mRNA substratePrecursor messenger RNAProtein-protein contactsC-terminal regionSaccharomyces cerevisiaeHeteroheptameric ringMature mRNAActive siteU6 snRNPsMRNA decayNuclear RNAPost-transcriptionallySpliceosomeLsm2Prp24SnRNPMessenger RNARNAMRNAIntronLSm8The life of U6 small nuclear RNA, from cradle to grave
Didychuk A, Butcher S, Brow D. The life of U6 small nuclear RNA, from cradle to grave. RNA 2018, 24: 437-460. PMID: 29367453, PMCID: PMC5855946, DOI: 10.1261/rna.065136.117.Peer-Reviewed Original ResearchConceptsU6 small nuclear RNASmall nuclear RNAPre-mRNANuclear RNAProcess of RNA splicingCatalyzes intron removalEukaryotic gene expressionPre-mRNA substrateUridine-rich small nuclear RNAsRemoval of intronsPrecursor messenger RNACryo-EM structureSplicing cycleNoncoding transcriptsCatalytic coreProtein partnersRNA splicingIntron removalSplice siteGenetic dataMacromolecular machinesSpliceosomeGene expressionSplicingConformational changes
2016
Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea
Lakshmanan V, Bansal D, Kulkarni J, Poduval D, Krishna S, Sasidharan V, Anand P, Seshasayee A, Palakodeti D. Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea. G3: Genes, Genomes, Genetics 2016, 6: 3035-3048. PMID: 27489207, PMCID: PMC5068929, DOI: 10.1534/g3.116.031120.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsAnimalsComputational BiologyGenome-Wide Association StudyGenome, HelminthHigh-Throughput Nucleotide SequencingMicroRNAsMolecular Sequence AnnotationPlatyhelminthsPoly APolyadenylationReproducibility of ResultsRNA InterferenceRNA Processing, Post-TranscriptionalRNA, MessengerConceptsSchmidtea mediterraneaAdvent of next-generation sequencing technologiesNext-generation sequencing technologiesGene expressionTissue-specific expression patternsMiRNA mediated gene regulationGenome-wide scaleGenome-wide analysisPoly(A) sitePosttranscriptional gene expressionRegulate posttranscriptional gene expressionGene annotationInternal exonsPolyadenylated transcriptsTranscript isoformsPolyadenylation eventsDegradome sequencingProtein domainsSequencing technologiesPre-mRNAGene regulationCoding sequenceIdeal model systemStem cell functionFreshwater planarians
2012
U1-Small Nuclear Ribonucleoprotein Activates the NLRP3 Inflammasome in Human Monocytes
Shin MS, Kang Y, Lee N, Kim SH, Kang KS, Lazova R, Kang I. U1-Small Nuclear Ribonucleoprotein Activates the NLRP3 Inflammasome in Human Monocytes. The Journal Of Immunology 2012, 188: 4769-4775. PMID: 22490866, PMCID: PMC3347773, DOI: 10.4049/jimmunol.1103355.Peer-Reviewed Original ResearchConceptsU1 snRNPNuclear ribonucleoproteinSystemic lupus erythematosusIL-1β productionU1 small nuclear RNAU1 small nuclear ribonucleoproteinSmall nuclear ribonucleoproteinCytosolic protein complexesLupus erythematosusAutoimmune diseasesProtein complexesMicrobial nucleic acidsNuclear RNAPre-mRNAHuman monocytesNOD-like receptor familyReactive oxygen speciesEndogenous DNAReceptor familyMolecular complexesOxygen speciesRibonucleoproteinTLR7/8 pathwayIL-1βNuclear moleculesU1-snRNP activates the NLRP3 inflammasome in human monocytes (171.7)
Shin M, Kang Y, Lee N, Kang K, Lazova R, Kang I. U1-snRNP activates the NLRP3 inflammasome in human monocytes (171.7). The Journal Of Immunology 2012, 188: 171.7-171.7. DOI: 10.4049/jimmunol.188.supp.171.7.Peer-Reviewed Original ResearchSystemic lupus erythematosusIL-1β productionU1 snRNPAutoimmune diseasesIL-1βCaspase-1Human monocytesReactive oxygen speciesU1 small nuclear RNAU1 small nuclear ribonucleoproteinCytosolic protein complexesLupus erythematosusNLRP3 inflammasomeMicrobial nucleic acidsNLRP3Protein complexesNuclear RNANuclear ribonucleoproteinPre-mRNAEndogenous DNAMonocytesAntibodiesPotential roleCD14Inflammasome
2007
U2 snRNP Binds Intronless Histone Pre-mRNAs to Facilitate U7-snRNP-Dependent 3′ End Formation
Friend K, Lovejoy AF, Steitz JA. U2 snRNP Binds Intronless Histone Pre-mRNAs to Facilitate U7-snRNP-Dependent 3′ End Formation. Molecular Cell 2007, 28: 240-252. PMID: 17964263, PMCID: PMC2149891, DOI: 10.1016/j.molcel.2007.09.026.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCell NucleusDEAD-box RNA HelicasesHeLa CellsHistonesHumansIntronsMiceModels, MolecularOocytesProtein ConformationRibonucleoprotein, U2 Small NuclearRibonucleoprotein, U7 Small NuclearRibonucleoproteins, Small NuclearRNA 3' End ProcessingRNA PrecursorsRNA-Binding ProteinsRNA, MessengerTime FactorsXenopus laevis
2004
An Intronic Enhancer Regulates Splicing of the Twintron of Drosophila melanogaster prospero Pre-mRNA by Two Different Spliceosomes
Scamborova P, Wong A, Steitz JA. An Intronic Enhancer Regulates Splicing of the Twintron of Drosophila melanogaster prospero Pre-mRNA by Two Different Spliceosomes. Molecular And Cellular Biology 2004, 24: 1855-1869. PMID: 14966268, PMCID: PMC350559, DOI: 10.1128/mcb.24.5.1855-1869.2004.Peer-Reviewed Original ResearchConceptsPurine-rich elementSplicing pathwaySplice siteU12-type spliceosomeU12-type splicingVitro splicing systemForms of mRNAAlternative splicingEarly embryogenesisKc cellsIntron sequencesPre-mRNASystematic deletionIntronic enhancerSplicingSequence requirementsIntron regionsEnhancer elementsNucleotides downstreamMolecular mechanismsTwintronSpliceosomeSplicing systemMutation analysisPathway
1998
Exonic Sequences in the 5′ Untranslated Region of α-Tubulin mRNA Modulate trans Splicing in Trypanosoma brucei
López-Estraño C, Tschudi C, Ullu E. Exonic Sequences in the 5′ Untranslated Region of α-Tubulin mRNA Modulate trans Splicing in Trypanosoma brucei. Molecular And Cellular Biology 1998, 18: 4620-4628. PMID: 9671472, PMCID: PMC109048, DOI: 10.1128/mcb.18.8.4620.Peer-Reviewed Original Research
1997
A new strategy for introducing photoactivatable 4-thiouridine ((4S)U) into specific positions in a long RNA molecule.
Yu YT, Steitz JA. A new strategy for introducing photoactivatable 4-thiouridine ((4S)U) into specific positions in a long RNA molecule. RNA 1997, 3: 807-10. PMID: 9214662, PMCID: PMC1369526.Peer-Reviewed Original ResearchConceptsPre-mRNAPre-mRNA substrateAT-AC intronsPhage RNA polymeraseRNA-DNA chimerasFull-length RNALong RNA moleculesRNA polymeraseRNA moleculesT4 RNA ligaseT4 DNA ligaseRNA ligaseDNA ligaseRNARNase H cleavageLigaseSpecific sitesSpecific positionsIntronsPolymeraseChimerasNew strategyCleavageOligonucleotideH cleavageDistribution of pre-mRNA splicing factors at sites of RNA polymerase II transcription.
Neugebauer K, Roth M. Distribution of pre-mRNA splicing factors at sites of RNA polymerase II transcription. Genes & Development 1997, 11: 1148-1159. PMID: 9159396, DOI: 10.1101/gad.11.9.1148.Peer-Reviewed Original ResearchMeSH KeywordsAntibodies, MonoclonalBinding SitesCell NucleusFluorescent Antibody Technique, IndirectHeLa CellsHumansNuclear ProteinsPhosphoproteinsRibonucleoproteins, Small NuclearRNA Polymerase IIRNA PrecursorsRNA SplicingRNA-Binding ProteinsSerine-Arginine Splicing FactorsTranscription, GeneticUridine TriphosphateConceptsRNA polymerase II transcriptionPolymerase II transcriptionMRNA splicing factorsSplicing factorsSR familyPre-mRNA splicingVisualization of hundredsHeLa cell nucleiSplicing regulatorsActive genesTranscription unitMRNA splicingGene regulatorsGene transcriptionPre-mRNADistinct functionsRNA synthesisTranscriptionCell nucleiSplicingSingle memberRegulatorActive site
1996
Length suppression in histone messenger RNA 3′-end maturation: Processing defects of insertion mutant premessenger RNAs can be compensated by insertions into the U7 small nuclear RNA
Scharl E, Steitz J. Length suppression in histone messenger RNA 3′-end maturation: Processing defects of insertion mutant premessenger RNAs can be compensated by insertions into the U7 small nuclear RNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 1996, 93: 14659-14664. PMID: 8962110, PMCID: PMC26191, DOI: 10.1073/pnas.93.25.14659.Peer-Reviewed Original ResearchConceptsHistone downstream elementU7 RNAHistone messenger RNASmall nuclear RNARNA processing systemSmall ribonucleoproteinPremessenger RNANuclear RNAPre-mRNAU7 small nuclear RNADownstream elementsCleavage siteRNAMessenger RNAXenopus oocytesBase pairingProcessing defectsU7First demonstrationHistonesRNAsRibonucleoproteinInsertionMRNASitesTrans -splicing in trypanosotnatid protozoa
Ullu E, Tschudi C, Gunzl A. Trans -splicing in trypanosotnatid protozoa. 1996, 115-133. DOI: 10.1093/oso/9780199636020.003.0007.Peer-Reviewed Original ResearchTrans splicingSplice siteT. brucei cellsPolycistronic pre-mRNARNA processing reactionsEnd of transcriptsDifferent variant surface glycoproteinsSeparate RNA moleculesVariant surface glycoproteinSL RNAList of organismsSmall RNAsBrucei cellsSL sequenceTrypanosomatid protozoaMature mRNALeader RNAMature speciesPre-mRNATrypanosoma bruceiRNA moleculesProcessing reactionsRNASurface glycoproteinFirst evidenceA Novel Spliceosome Containing U11, U12, and U5 snRNPs Excises a Minor Class (AT–AC) Intron In Vitro
Tarn W, Steitz J. A Novel Spliceosome Containing U11, U12, and U5 snRNPs Excises a Minor Class (AT–AC) Intron In Vitro. Cell 1996, 84: 801-811. PMID: 8625417, DOI: 10.1016/s0092-8674(00)81057-0.Peer-Reviewed Original ResearchMeSH KeywordsBase CompositionBase SequenceBlotting, NorthernCell NucleusHeLa CellsHumansMolecular Sequence DataNucleic Acid ConformationOligodeoxyribonucleotidesPlasmidsPolymerase Chain ReactionRibonuclease HRibonucleoprotein, U5 Small NuclearRibonucleoproteins, Small NuclearRNA PrecursorsRNA SplicingConceptsU5 small nuclear ribonucleoproteinSmall nuclear ribonucleoproteinU12 small nuclear ribonucleoproteinsMinor class intronsProtein coding genesPre-mRNA substrateNative gel electrophoresisCoding genesBranch site sequenceSplicing complexesNuclear ribonucleoproteinPre-mRNAP120 geneLariat intermediateSite sequenceIntronsHeLa cellsEssential roleSplicingGel electrophoresisBranch siteGenesU12Minor classU11
1995
Structure and function of hnRNP proteins
Kiledjian M, Burd C, Gorlach M, Portman D, Dreyfuss G. Structure and function of hnRNP proteins. 1995, 127-149. DOI: 10.1093/oso/9780199635054.003.0006.Peer-Reviewed Original ResearchHnRNP proteinsEukaryotic RNA polymerase IIRNA-processing reactionsRNA polymerase IIRNA-binding proteinNascent transcriptsPolymerase IIHnRNP complexesTranscription complexPrimary transcriptCytoplasmic mRNAPre-mRNAMRNA moleculesGene expressionProteinMRNATranscriptsSeries of eventsNuclear structureComplexesIntransHnRNAsStable componentCytoplasmPathway
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