2025
Comprehensive mutational analysis of the sequence–function relationship within a viral internal ribosome entry site
Grunseich S, Strobel S. Comprehensive mutational analysis of the sequence–function relationship within a viral internal ribosome entry site. Nucleic Acids Research 2025, 53: gkaf445. PMID: 40421802, PMCID: PMC12107430, DOI: 10.1093/nar/gkaf445.Peer-Reviewed Original ResearchConceptsCrPV-IRESIRES functionViral internal ribosome entry siteNext-generation sequencing methodsInternal ribosome entry siteSequence-function relationshipsCricket paralysis virusRibosome entry siteCell-free systemComprehensive mutational analysisMechanism of translationHigh-throughput methodRibosome contactsIntergenic regionRNA elementsTranslation initiationSequence requirementsIRES elementsMutation databaseEukaryotic extractsInitiation factorsSequencing methodsExpressed proteinsHelical regionsMutation analysisGuidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR)
Loughran G, Andreev D, Terenin I, Namy O, Mikl M, Yordanova M, McManus C, Firth A, Atkins J, Fraser C, Ignatova Z, Iwasaki S, Kufel J, Larsson O, Leidel S, Mankin A, Mariotti M, Tanenbaum M, Topisirovic I, Vázquez-Laslop N, Viero G, Caliskan N, Chen Y, Clark P, Dinman J, Farabaugh P, Gilbert W, Ivanov P, Kieft J, Mühlemann O, Sachs M, Shatsky I, Sonenberg N, Steckelberg A, Willis A, Woodside M, Valasek L, Dmitriev S, Baranov P. Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR). Nature Structural & Molecular Biology 2025, 32: 418-430. PMID: 40033152, DOI: 10.1038/s41594-025-01492-x.Peer-Reviewed Original ResearchConceptsInternal ribosome entry siteGene expression reportersStop codon readthroughRibosome entry siteEukaryotic translationTranscription initiationAntisense transcriptsRegulatory elementsRibosomal frameshiftingCodon readthroughExpression reportersEntry siteDual reportersUnconventional mechanismSequencePolyadenylationMisinterpretation of dataExpressionReadthroughFrameshiftSplicingTranscriptionEvaluate published dataMinimal requirementsProtein
2007
Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR
Lytle JR, Yario TA, Steitz JA. Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR. Proceedings Of The National Academy Of Sciences Of The United States Of America 2007, 104: 9667-9672. PMID: 17535905, PMCID: PMC1887587, DOI: 10.1073/pnas.0703820104.Peer-Reviewed Original ResearchConceptsInternal ribosome entry siteTarget mRNAsMiRNA-mediated repressionRepression of translationLuciferase reporter mRNAMiRNA target sitesInitiation of translationMiRNA-binding sitesHuman HeLa cellsRibosome entry siteMicroRNA-binding sitesLet-7 complementary sitesHuman Ago2Reporter mRNAMicroRNAs (miRNAs) bindEndogenous mRNATranslational efficiencyLet-7a miRNAUTRProtein synthesisDNA transfectionComplementary sitesHeLa cellsEntry siteTarget site
2003
Eukaryotic Initiation Factors 4G and 4A Mediate Conformational Changes Downstream of the Initiation Codon of the Encephalomyocarditis Virus Internal Ribosomal Entry Site
Kolupaeva VG, Lomakin IB, Pestova TV, Hellen CU. Eukaryotic Initiation Factors 4G and 4A Mediate Conformational Changes Downstream of the Initiation Codon of the Encephalomyocarditis Virus Internal Ribosomal Entry Site. Molecular And Cellular Biology 2003, 23: 687-698. PMID: 12509466, PMCID: PMC151537, DOI: 10.1128/mcb.23.2.687-698.2003.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateBase SequenceBinding SitesCodon, InitiatorEncephalomyocarditis virusEscherichia coliEukaryotic Initiation Factor-4AEukaryotic Initiation Factor-4GGene DeletionModels, BiologicalModels, MolecularMolecular Sequence DataPlasmidsProtein BindingProtein BiosynthesisProtein ConformationProtein Structure, SecondaryProtein Structure, TertiaryRibosomesRNASequence Homology, Nucleic AcidConceptsInternal ribosome entry siteEukaryotic initiation factor 2EIF4GCentral domainEukaryotic initiation factor 4GConformational changesInitiation factor 2K domainRibosome binding siteInitiation of translationInternal ribosomal entry siteEntry siteExtensive conformational rearrangementsThree-way helical junctionInitiation codon AUGRibosome entry siteEncephalomyocarditis virus internal ribosomal entry siteEncephalomyocarditis virus (EMCV) mRNAInitiation codonRibosomal complexesC-terminusIRES functionProductive bindingCodon AUGN-terminus
2002
Vitamin B12 Stalls the 80S Ribosomal Complex on the Hepatitis C Internal Ribosome Entry Site
Takyar S, Gowans E, Lott W. Vitamin B12 Stalls the 80S Ribosomal Complex on the Hepatitis C Internal Ribosome Entry Site. Journal Of Molecular Biology 2002, 319: 1-8. PMID: 12051931, DOI: 10.1016/s0022-2836(02)00300-5.Peer-Reviewed Original ResearchConceptsIRES-dependent translationRibosome entry siteHepatitis C virus internal ribosome entry siteInternal ribosome entry siteEntry siteTranslation inhibitor cycloheximideS ribosomal complexCap-dependent mRNAMRNA-specificGradient centrifugation analysisSucrose gradient centrifugation analysisCompetitive binding mechanismHCV IRESRibosomal complexesTranslation inhibitorsInhibitor cycloheximideCentrifugation analysisMRNAComplex formationCycloheximideBinding mechanism
2001
A Conserved HEAT Domain within eIF4G Directs Assembly of the Translation Initiation Machinery
Marcotrigiano J, Lomakin I, Sonenberg N, Pestova T, Hellen C, Burley S. A Conserved HEAT Domain within eIF4G Directs Assembly of the Translation Initiation Machinery. Molecular Cell 2001, 7: 193-203. PMID: 11172724, DOI: 10.1016/s1097-2765(01)00167-8.Peer-Reviewed Original ResearchConceptsInternal ribosome entry siteTranslation initiation machineryInitiation machineryHEAT domainATP-dependent RNA helicase eIF4AStructure-based site-directed mutagenesisCap-independent translation initiationRNA helicase eIF4ASite-directed mutagenesisPicornaviral internal ribosome-entry siteRibosome entry siteRibosomal complex formationHelicase eIF4ATranslation initiationAlpha-helixEntry siteEIF4AMechanistic insightsX-ray structureComplex formationMachineryBiochemical resultsEssential componentDomainMutagenesis
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