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 RNACo-transcriptional gene regulation in eukaryotes and prokaryotes
Shine M, Gordon J, Schärfen L, Zigackova D, Herzel L, Neugebauer K. Co-transcriptional gene regulation in eukaryotes and prokaryotes. Nature Reviews Molecular Cell Biology 2024, 25: 534-554. PMID: 38509203, PMCID: PMC11199108, DOI: 10.1038/s41580-024-00706-2.Peer-Reviewed Original ResearchRNA polymeraseRNA biogenesisRNA processingGene regulationDevelopment of RNA sequencingTranscription to translationRNA processing intermediatesGene expression stepsCo-transcriptional activityCellular stress responseNascent RNATranscriptional readthroughNascent transcriptsTranscriptional coordinationIntron retentionRNA foldingEukaryotesProkaryotesExpression stepsRNA sequencingTransient transcriptionGene expressionTranscriptionStress responseRNAA compact regulatory RNA element in mouse Hsp70 mRNA
Wang W, Liu F, Ugalde M, Pyle A. A compact regulatory RNA element in mouse Hsp70 mRNA. NAR Molecular Medicine 2024, 1: ugae002. PMID: 38318492, PMCID: PMC10840451, DOI: 10.1093/narmme/ugae002.Peer-Reviewed Original ResearchOpen reading frameRNA elementsHeat shockOpen reading frame sequenceRegulatory RNA elementsSecondary structure modelMessenger RNACap-independent mannerCap-dependent translationMolecular chaperone functionSequences of HSP70Reading frameMisfolded proteinsRNA foldingRegulate protein expressionChaperone functionMRNA sequencesUntranslated regionShort stretchSecondary structureCell stressGene expressionHSP70 gene expressionStructural basisMolecular mechanisms
2022
An in Vitro Cytomimetic of In‐Cell RNA Folding
Yoo H, Davis C. An in Vitro Cytomimetic of In‐Cell RNA Folding. ChemBioChem 2022, 23: e202200406. PMID: 35999178, DOI: 10.1002/cbic.202200406.Peer-Reviewed Original Research
2018
Analyses of mRNA structure dynamics identify embryonic gene regulatory programs
Beaudoin JD, Novoa EM, Vejnar CE, Yartseva V, Takacs CM, Kellis M, Giraldez AJ. Analyses of mRNA structure dynamics identify embryonic gene regulatory programs. Nature Structural & Molecular Biology 2018, 25: 677-686. PMID: 30061596, PMCID: PMC6690192, DOI: 10.1038/s41594-018-0091-z.Peer-Reviewed Original ResearchConceptsGene regulatory programsUntranslated regionRegulatory programsKey maternal factorsZygotic transitionZebrafish developmentGene functionRNA functionRegulatory elementsGene expressionRNA structureRNA foldingBiological transitionsStructure dynamicsCentral roleCrucial roleCellular systemsRemodelersTranscriptomeRibosomesVivoGenesFoldingCCNA1Role
2014
Principles of ion recognition in RNA: insights from the group II intron structures
Marcia M, Pyle AM. Principles of ion recognition in RNA: insights from the group II intron structures. RNA 2014, 20: 516-527. PMID: 24570483, PMCID: PMC3964913, DOI: 10.1261/rna.043414.113.Peer-Reviewed Original ResearchConceptsActive siteSite-bound ionsIon recognitionMetal ionsOrganic ionsLatter ionIon-binding sitesCatalytic ionsCrystal structureGU wobble pairsMonovalent ionsLarge RNA moleculesIonsStructural ionsBiophysical methodsGroup II intron structureGA mismatchesLong-range tertiary contactsRNA structureRNA foldingTertiary contactsWobble pairStructureCatalysisHeteronuclear
2011
Small Ribonucleoproteins in Ribosome Biogenesis
Bleichert F, Baserga S. Small Ribonucleoproteins in Ribosome Biogenesis. Protein Reviews 2011, 135-156. DOI: 10.1007/978-1-4614-0514-6_7.ChaptersSmall nucleolar RNPsSite of functionNon-enzymatic functionsRibosome biogenesisFunctional ribosomesEukaryotic cellsSmall ribonucleoproteinSmall RNPsGuide RNANucleotide modificationsRNA componentRNA substratesSubstrate RNAEndonucleolytic cleavageMacromolecular assembliesRNA foldingCurrent understandingRNARNPNucleoliEnzymeLarge macromoleculesAssemblyChaperonesBiogenesis
2009
Tertiary architecture of the Oceanobacillus iheyensis group II intron
Toor N, Keating KS, Fedorova O, Rajashankar K, Wang J, Pyle AM. Tertiary architecture of the Oceanobacillus iheyensis group II intron. RNA 2009, 16: 57-69. PMID: 19952115, PMCID: PMC2802037, DOI: 10.1261/rna.1844010.Peer-Reviewed Original ResearchConceptsGroup II intronsPotential evolutionary relationshipsGroup II intron structureGroup IIC intronIntron structureEvolutionary relationshipsEukaryotic spliceosomeInteraction networksRNA moleculesIntronsTertiary structural organizationGenetic studiesRibose zipperRNA foldingTertiary interactionsLarge ribozymesInteraction nodesStructural organizationTertiary architectureEukaryotesSpliceosomeGene therapyGenomeZipperFolding
1999
An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site
Szewczak A, Ortoleva-Donnelly L, Zivarts M, Oyelere A, Kazantsev A, Strobel S. An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site. Proceedings Of The National Academy Of Sciences Of The United States Of America 1999, 96: 11183-11188. PMID: 10500151, PMCID: PMC18008, DOI: 10.1073/pnas.96.20.11183.Peer-Reviewed Original ResearchConceptsHelix dockingBase triplesRecognition surfaceGroup I intronActive siteNetwork of interactionsTetrahymena group IP3 helixStructural biologySubstrate bindingI intronCatalytic RNAProduct bindingSuppression analysisFunctional importanceRNA foldingRNA constructsSubstrate helixBiochemical evidenceMutant ribozymesRibozyme active siteSubstantial rearrangementHelixCrystallographic modelRibozyme
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply