2024
Alternative translation initiation produces synaptic organizer proteoforms with distinct localization and functions
Lee P, Sun Y, Soares A, Fai C, Picciotto M, Guo J. Alternative translation initiation produces synaptic organizer proteoforms with distinct localization and functions. Molecular Cell 2024, 84: 3967-3978.e8. PMID: 39317199, PMCID: PMC11490368, DOI: 10.1016/j.molcel.2024.08.032.Peer-Reviewed Original ResearchTranslation initiation siteNeuronal pentraxin receptorAUG translational initiation siteAlternative translation initiation sitesN-terminal signal sequenceN-terminal transmembrane domainRNA secondary structureAlternative translation initiationN-terminal extensionTranslation initiationSignal sequenceProtein isoformsProtein localizationAUG initiatorTransmembrane domainWidespread mechanismSecondary structureInitiation siteAlternative usageAMPA-type glutamate receptorsProteoformsSecreted factorsProteinReduced AMPA receptorMRNA
2023
Genome-wide CRISPR screens identify noncanonical translation factor eIF2A as an enhancer of SARS-CoV-2 programmed −1 ribosomal frameshifting
Wei L, Sun Y, Guo J. Genome-wide CRISPR screens identify noncanonical translation factor eIF2A as an enhancer of SARS-CoV-2 programmed −1 ribosomal frameshifting. Cell Reports 2023, 42: 112987. PMID: 37581984, DOI: 10.1016/j.celrep.2023.112987.Peer-Reviewed Original ResearchConceptsSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Respiratory syndrome coronavirus 2Host factorsSARS-CoV-2 replicationSyndrome coronavirus 2SARS-CoV-2Eukaryotic translation initiation factor 2ACoronavirus 2Viral RNAGenome-wide CRISPR screenFactor 2APositive-strand RNA virusesGenome-wide CRISPRRNA virusesKnockout screensRNAInitiationStress promotes RNA G-quadruplex folding in human cells
Kharel P, Fay M, Manasova E, Anderson P, Kurkin A, Guo J, Ivanov P. Stress promotes RNA G-quadruplex folding in human cells. Nature Communications 2023, 14: 205. PMID: 36639366, PMCID: PMC9839774, DOI: 10.1038/s41467-023-35811-x.Peer-Reviewed Original ResearchConceptsHuman cellsMRNA stabilityCellular stress responseRG4 structuresG-quadruplex structuresRNA G4sDynamic regulationG-quadruplex foldingRich nucleic acidsStress responsePermissive conditionsRG4FoldingStress removalRegulatory impactNucleic acidsCellsDimethylsulfateRNAMotifGuanineMRNARegulationStressSequence
2022
Systematic generation and imaging of tandem repeats reveal base-pairing properties that promote RNA aggregation
Isiktas A, Eshov A, Yang S, Guo J. Systematic generation and imaging of tandem repeats reveal base-pairing properties that promote RNA aggregation. Cell Reports Methods 2022, 2: 100334. PMID: 36452875, PMCID: PMC9701603, DOI: 10.1016/j.crmeth.2022.100334.Peer-Reviewed Original ResearchConceptsBase pairsRNA aggregationRNA-RNA interactionsLive-cell imagingConsecutive base pairsNoncanonical base pairsRNA aggregatesRepeat RNARepeat DNAMolecular basisRepeat sequencesMolecular mechanismsTandem repeatsRNAHexanucleotide repeatsStructural determinantsGGGGCC hexanucleotide repeatBase-pairing propertiesCommon pathological featureRepeatsSequenceUnifying modelGeneralizable approachDistinct propertiesEnhanced aggregationSecondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells
Lan TCT, Allan MF, Malsick LE, Woo JZ, Zhu C, Zhang F, Khandwala S, Nyeo SSY, Sun Y, Guo JU, Bathe M, Näär A, Griffiths A, Rouskin S. Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells. Nature Communications 2022, 13: 1128. PMID: 35236847, PMCID: PMC8891300, DOI: 10.1038/s41467-022-28603-2.Peer-Reviewed Original ResearchConceptsRNA genomeSARS-CoV-2 RNA genomeStructural ensemblesAlternative RNA conformationsSingle-nucleotide resolutionInfected cellsRNA biologyGenomic structureSARS-CoV-2 genomeCellular contextNucleotide resolutionFunctional characterizationGenomeRNA conformationEntire SARS-CoV-2 genomeProfiling studiesFull lengthRNAStimulation elementCellsBiologyBetacoronavirusesLittle experimental dataConformationPromotes
2021
Restriction of SARS-CoV-2 replication by targeting programmed −1 ribosomal frameshifting
Sun Y, Abriola L, Niederer RO, Pedersen SF, Alfajaro MM, Silva Monteiro V, Wilen CB, Ho YC, Gilbert WV, Surovtseva YV, Lindenbach BD, Guo JU. Restriction of SARS-CoV-2 replication by targeting programmed −1 ribosomal frameshifting. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2023051118. PMID: 34185680, PMCID: PMC8256030, DOI: 10.1073/pnas.2023051118.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 replicationSARS-CoV-2Severe acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Respiratory syndrome coronavirus 2Syndrome coronavirus 2Vero E6 cellsHigh-throughput compound screenOpen reading frame 1bEffective antiviral strategiesCoronavirus 2E6 cellsAntiviral strategiesViral gene expressionCompound screenFluoroquinolone antibacterialsFrame 1bGene expressionRegulation of nonsense-mediated mRNA decay in neural development and disease
Lee PJ, Yang S, Sun Y, Guo JU. Regulation of nonsense-mediated mRNA decay in neural development and disease. Journal Of Molecular Cell Biology 2021, 13: 269-281. PMID: 33783512, PMCID: PMC8339359, DOI: 10.1093/jmcb/mjab022.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsAberrant mRNAsNonsense-mediated mRNA decayMRNA decay functionCore NMD factorsMRNA surveillance mechanismGene regulation mechanismsQuality control mechanismsPremature termination codonNMD factorsPhysiological mRNAsOrganismal levelMRNA decayDevelopmental regulationGenetic evidenceMolecular basisTermination codonBiological functionsRegulation mechanismNeural developmentPhysiological functionsSurveillance mechanismNMDNeurodegenerative diseasesMRNACritical role
2020
C9orf72 arginine-rich dipeptide repeats inhibit UPF1-mediated RNA decay via translational repression
Sun Y, Eshov A, Zhou J, Isiktas AU, Guo JU. C9orf72 arginine-rich dipeptide repeats inhibit UPF1-mediated RNA decay via translational repression. Nature Communications 2020, 11: 3354. PMID: 32620797, PMCID: PMC7335171, DOI: 10.1038/s41467-020-17129-0.Peer-Reviewed Original ResearchMeSH KeywordsAmyotrophic Lateral SclerosisAnimalsC9orf72 ProteinCell Line, TumorCell SurvivalDatasets as TopicDNA Repeat ExpansionEmbryo, MammalianFemaleFrontal LobeFrontotemporal DementiaHumansIntronsMiceNeuronsNonsense Mediated mRNA DecayPrimary Cell CultureProtein BiosynthesisRNA HelicasesRNA-SeqRNA, MessengerTrans-ActivatorsConceptsArginine-rich dipeptide repeatsNonsense-mediated decayRNA surveillanceTranslational repressionNMD inhibitionDipeptide repeatsRNA Decay mechanismsGlobal translational repressionStress granule formationC9ALS/FTDRNA decayFrameshift 1Repeat regionFamilial amyotrophic lateral sclerosisGranule formationCultured cellsFTD brainC9orf72 geneRepressionSurvival of neuronsRepeatsAmyotrophic lateral sclerosisMutantsGenesLateral sclerosisCoding functions of “noncoding” RNAs
Wei LH, Guo JU. Coding functions of “noncoding” RNAs. Science 2020, 367: 1074-1075. PMID: 32139529, DOI: 10.1126/science.aba6117.Commentaries, Editorials and LettersConceptsRNA regionsProtein-coding functionProtein-coding sequencesDistinct biological processesRNA sequencing studiesLong noncoding RNAPervasive transcriptionFunctional peptidesPervasive translationHuman genomeNoncoding RNAsTranslation eventsBiological processesSequencing studiesCell growthRNATranscriptomeGenomeTranscriptionLncRNAsPeptidesMicroproteinsTranslationSubsequent studiesRegion
2016
RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria.
Guo JU, Bartel DP. RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria. Science (New York, N.Y.) 2016, 353 PMID: 27708011, PMCID: PMC5367264, DOI: 10.1126/science.aaf5371.Peer-Reviewed Original Research
2014
Expanded identification and characterization of mammalian circular RNAs.
Guo JU, Agarwal V, Guo H, Bartel DP. Expanded identification and characterization of mammalian circular RNAs. Genome Biology 2014, 15: 409. PMID: 25070500, PMCID: PMC4165365, DOI: 10.1186/s13059-014-0409-z.Peer-Reviewed Original ResearchDistribution, recognition and regulation of non-CpG methylation in the adult mammalian brain.
Guo JU, Su Y, Shin JH, Shin J, Li H, Xie B, Zhong C, Hu S, Le T, Fan G, Zhu H, Chang Q, Gao Y, Ming GL, Song H. Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nature Neuroscience 2014, 17: 215-22. PMID: 24362762, PMCID: PMC3970219, DOI: 10.1038/nn.3607.Peer-Reviewed Original Research
2012
Neuronal activation and insight into the plasticity of DNA methylation.
Felling RJ, Guo JU, Song H. Neuronal activation and insight into the plasticity of DNA methylation. Epigenomics 2012, 4: 125-7. PMID: 22449183, DOI: 10.2217/epi.12.2.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
2011
Interaction between FEZ1 and DISC1 in regulation of neuronal development and risk for schizophrenia.
Kang E, Burdick KE, Kim JY, Duan X, Guo JU, Sailor KA, Jung DE, Ganesan S, Choi S, Pradhan D, Lu B, Avramopoulos D, Christian K, Malhotra AK, Song H, Ming GL. Interaction between FEZ1 and DISC1 in regulation of neuronal development and risk for schizophrenia. Neuron 2011, 72: 559-71. PMID: 22099459, DOI: 10.1016/j.neuron.2011.09.032.Peer-Reviewed Original ResearchNeuronal activity modifies the DNA methylation landscape in the adult brain.
Guo JU, Ma DK, Mo H, Ball MP, Jang MH, Bonaguidi MA, Balazer JA, Eaves HL, Xie B, Ford E, Zhang K, Ming GL, Gao Y, Song H. Neuronal activity modifies the DNA methylation landscape in the adult brain. Nature Neuroscience 2011, 14: 1345-51. PMID: 21874013, PMCID: PMC3183401, DOI: 10.1038/nn.2900.Peer-Reviewed Original ResearchHydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain.
Guo JU, Su Y, Zhong C, Ming GL, Song H. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 2011, 145: 423-34. PMID: 21496894, PMCID: PMC3088758, DOI: 10.1016/j.cell.2011.03.022.Peer-Reviewed Original Research
2010
Epigenetic choreographers of neurogenesis in the adult mammalian brain.
Ma DK, Marchetto MC, Guo JU, Ming GL, Gage FH, Song H. Epigenetic choreographers of neurogenesis in the adult mammalian brain. Nat Neurosci 2010, 13: 1338-44. PMID: 20975758, DOI: 10.1038/nn.2672.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
2009
DISC1 regulates new neuron development in the adult brain via modulation of AKT-mTOR signaling through KIAA1212.
Kim JY, Duan X, Liu CY, Jang MH, Guo JU, Pow-anpongkul N, Kang E, Song H, Ming GL. DISC1 regulates new neuron development in the adult brain via modulation of AKT-mTOR signaling through KIAA1212. Neuron 2009, 63: 761-73. PMID: 19778506, DOI: 10.1016/j.neuron.2009.08.008.Peer-Reviewed Original Research