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
Secondary 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
Regulation 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 J, Bartel D. RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria. Science 2016, 353: aaf5371-aaf5371. PMID: 27708011, PMCID: PMC5367264, DOI: 10.1126/science.aaf5371.Peer-Reviewed Original ResearchConceptsRNA G-quadruplexesEukaryotic cellsG-quadruplexStable four-stranded structuresG-quadruplexes in vitroG-quadruplex-forming sequencesPosttranscriptional gene regulationG-quadruplex-forming regionsFour-stranded structuresBacterial transcriptomesRNA regionsGene regulationEscherichia coliImpaired translationRNABacteriaCellsIn vitroEukaryotesTranscriptomeSequenceMachineryRegionRegulation
2014
Expanded identification and characterization of mammalian circular RNAs
Guo J, Agarwal V, Guo H, Bartel D. 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 ResearchConceptsRNA-seq dataRNA-seqHuman circRNAsProtein-coding sequencesZinc-finger proteinProperties of circRNAsRegulate gene expressionCell type-specificCircular RNAsSequence conservationENCODE projectRibosome profilingMiRNA sitesTopological isoformsComputational pipelineBiological functionsMouse circRNAsGene expressionMiR-7 spongeLow abundanceCell typesExpression levelsRNACircRNAsSequence
2013
Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain
Guo J, Su Y, Shin J, Shin J, Li H, Xie B, Zhong C, Hu S, Le T, Fan G, Zhu H, Chang Q, Gao Y, Ming G, Song H. Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nature Neuroscience 2013, 17: 215-222. PMID: 24362762, PMCID: PMC3970219, DOI: 10.1038/nn.3607.Peer-Reviewed Original ResearchConceptsCpH methylationNon-CpG cytosinesNon-CpG methylationSingle-base resolutionDNA methylome profilingDNA methyltransferase DNMT3ARepress transcriptionCpG dinucleotidesMethyltransferase DNMT3AProtein MeCP2DNANeuronal maturationMethylationMammalian brainDentate gyrus neuronsAdult mammalian brainCpGTranscriptionDinucleotideBisphenol A delays the perinatal chloride shift in cortical neurons by epigenetic effects on the Kcc2 promoter
Yeo M, Berglund K, Hanna M, Guo J, Kittur J, Torres M, Abramowitz J, Busciglio J, Gao Y, Birnbaumer L, Liedtke W. Bisphenol A delays the perinatal chloride shift in cortical neurons by epigenetic effects on the Kcc2 promoter. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 4315-4320. PMID: 23440186, PMCID: PMC3600491, DOI: 10.1073/pnas.1300959110.Peer-Reviewed Original ResearchMeSH KeywordsAir Pollutants, OccupationalAnimalsBenzhydryl CompoundsCells, CulturedCentral Nervous System DiseasesCerebral CortexChloridesDNA-Binding ProteinsEpigenesis, GeneticFemaleHistone Deacetylase 1HumansK Cl- CotransportersMaleMiceNerve Tissue ProteinsNeuronsPhenolsRatsResponse ElementsSex CharacteristicsSymportersConceptsEffects of bisphenol AKcc2 promoterBisphenol A exposureKCC2 expressionCortical neuronsHistone deacetylase 1Binding of methyl-CpG-binding protein 2Potassium-chloride cotransporter 2KCC2 gene expressionMethyl-CpG-binding protein 2Knockdown of histone deacetylase 1Sexually dimorphic mannerSexually dimorphic effectsHuman neurodevelopmental disordersBisphenol-A effectsHuman cortical neuronsToxic mechanisms of bisphenol ANeuronal chlorideCotransporter 2Cortical slicesBinding protein 2KCC2Mouse damsDimorphic mannerInterneuron migration
2012
Neuronal activation and insight into the plasticity of DNA methylation
Felling R, Guo J, Song H. Neuronal activation and insight into the plasticity of DNA methylation. Epigenomics 2012, 4: 125-127. PMID: 22449183, DOI: 10.2217/epi.12.2.Peer-Reviewed Original Research
2011
Interaction between FEZ1 and DISC1 in Regulation of Neuronal Development and Risk for Schizophrenia
Kang E, Burdick K, Kim J, Duan X, Guo J, Sailor K, Jung D, Ganesan S, Choi S, Pradhan D, Lu B, Avramopoulos D, Christian K, Malhotra A, Song H, Ming G. Interaction between FEZ1 and DISC1 in Regulation of Neuronal Development and Risk for Schizophrenia. Neuron 2011, 72: 559-571. PMID: 22099459, PMCID: PMC3222865, DOI: 10.1016/j.neuron.2011.09.032.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAdultAgedAnimalsCase-Control StudiesCells, CulturedFemaleGene Knockdown TechniquesGenetic Association StudiesHippocampusHumansMaleMiceMice, Inbred C57BLMiddle AgedNerve Tissue ProteinsNeurogenesisPolymorphism, Single NucleotideProtein BindingRisk FactorsSchizophreniaConceptsDisrupted-in-schizophrenia 1Neuronal developmentElongation protein zeta-1Genetic association analysisRegulate cell positioningRegulation of neuronal developmentDendritic growth of newborn neuronsNewborn neuronsEpistatic interactionsScaffold proteinAssociation analysisSchizophrenia 1Susceptibility genesIntracellular partnersCohort of schizophrenia patientsFEZ1Adult mouse hippocampusRisk of schizophreniaZeta 1Schizophrenia patientsHealthy controlsCell positionIncreased riskMouse hippocampusMental disordersEmerging roles of TET proteins and 5-hydroxymethylcytosines in active DNA demethylation and beyond
Guo J, Su Y, Zhong C, Ming G, Song H. Emerging roles of TET proteins and 5-hydroxymethylcytosines in active DNA demethylation and beyond. Cell Cycle 2011, 10: 2662-2668. PMID: 21811096, PMCID: PMC3219536, DOI: 10.4161/cc.10.16.17093.Peer-Reviewed Original ResearchHydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain
Guo J, Su Y, Zhong C, Ming G, Song H. Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain. Cell 2011, 145: 423-434. PMID: 21496894, PMCID: PMC3088758, DOI: 10.1016/j.cell.2011.03.022.Peer-Reviewed Original ResearchConceptsActive DNA demethylationDNA demethylationMammalian cellsHydroxylation of 5-methylcytosineMammalian genomic DNABase excision repair pathwayPromoter DNA demethylationHuman DNA glycosylasesExcision repair pathwayAdult mouse brain in vivoCytosine methylationEpigenetic marksTranscriptional regulationGenomic DNADNA glycosylaseRepair pathwaysCovalent modificationGene expressionMolecular mechanismsActivity-inducedCytidine deaminaseEnzymatic removalDemethylationTET1Mouse brain in vivo
2010
Epigenetic choreographers of neurogenesis in the adult mammalian brain
Ma D, Marchetto M, Guo J, Ming G, Gage F, Song H. Epigenetic choreographers of neurogenesis in the adult mammalian brain. Nature Neuroscience 2010, 13: 1338-1344. PMID: 20975758, PMCID: PMC3324277, DOI: 10.1038/nn.2672.Peer-Reviewed Original Research
2009
DISC1 Regulates New Neuron Development in the Adult Brain via Modulation of AKT-mTOR Signaling through KIAA1212
Kim J, Duan X, Liu C, Jang M, Guo J, Pow-anpongkul N, Kang E, Song H, Ming G. DISC1 Regulates New Neuron Development in the Adult Brain via Modulation of AKT-mTOR Signaling through KIAA1212. Neuron 2009, 63: 761-773. PMID: 19778506, PMCID: PMC3075620, DOI: 10.1016/j.neuron.2009.08.008.Peer-Reviewed Original ResearchMeSH KeywordsAdult Stem CellsAnalysis of VarianceAnimalsAnimals, NewbornCell MovementCells, CulturedFemaleGene Expression Regulation, DevelopmentalGene Knockdown TechniquesGreen Fluorescent ProteinsHippocampusHumansImmunoprecipitationImmunosuppressive AgentsMiceMice, Inbred C57BLNerve Tissue ProteinsNeurogenesisNeuronsOncogene Protein v-aktPregnancyProtein BindingRNA InterferenceSignal TransductionSirolimusTransfectionConceptsDisrupted-in-schizophrenia 1Susceptibility genesMammalian target of rapamycinNeuronal developmentAkt-binding partnersAkt downstream effectorsAkt signalingRegulate multiple aspectsAkt activation in vitroDisrupted-in-schizophreniaMultiple susceptibility genesPharmacological inhibition of mammalian target of rapamycinSchizophrenia susceptibility genesRegulate neuronal developmentSignaling of AktNeurons in vivoAkt-mTOR signaling pathwayInhibition of mammalian target of rapamycinBinding partnersAkt-mTOR signalingDownstream effectorsGenetic manipulationTarget of rapamycinActivity in vitroNewborn neuronsDNA excision repair proteins and Gadd45 as molecular players for active DNA demethylation
Ma D, Guo J, Ming G, Song H. DNA excision repair proteins and Gadd45 as molecular players for active DNA demethylation. Cell Cycle 2009, 8: 1526-1531. PMID: 19377292, PMCID: PMC2738863, DOI: 10.4161/cc.8.10.8500.Peer-Reviewed Original ResearchConceptsActive DNA demethylationDNA demethylationProcess of DNA demethylationMolecular playersProcess of DNA methylationHeritable gene silencingDNA cytosine methylationClass of methyltransferasesDNA demethylation mechanismTransgenerational epigenetic inheritanceDNA excision repair proteinNucleotide-excision repairExcision repair proteinsHeterochromatin formationCytosine methylationExcision repair enzymesEpigenetic inheritanceEvolutionary implicationsDNA methylationGene silencingModification signalsEnzymatic machineryDemethylation mechanismRepair enzymesRepair proteins
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