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
2020
Coding 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
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