2025
Human and pathogen-encoded circular RNAs in viral infections: insights into functions and therapeutic opportunities
Mueller N, Dujsikova A, Singh A, Chen Y. Human and pathogen-encoded circular RNAs in viral infections: insights into functions and therapeutic opportunities. Human Molecular Genetics 2025, ddaf031. PMID: 40304711, DOI: 10.1093/hmg/ddaf031.Peer-Reviewed Original ResearchDNA virusesHost cellular machineryHost-virus interactionsCircular RNAsContribution to pathogenesisRNA biologyProtein translationCellular machineryProtein decoysRNA-based therapiesBiological rolePotential of circRNAsRegulatory moleculesRNAMicroRNA spongesViral systemsDNAViral replicationImmune evasionTherapeutic targetCircRNAsTherapeutic opportunitiesHostProteinViral diseasesQKI-induced circ_0001766 inhibits colorectal cancer progression and rapamycin resistance by miR-1203/PPP1R3C/mTOR/Myc axis
Zhou Y, Gao Y, Peng Y, Cai C, Han Y, Chen Y, Deng G, Ouyang Y, Shen H, Zeng S, Du Y, Xiao Z. QKI-induced circ_0001766 inhibits colorectal cancer progression and rapamycin resistance by miR-1203/PPP1R3C/mTOR/Myc axis. Cell Death Discovery 2025, 11: 192. PMID: 40263288, PMCID: PMC12015279, DOI: 10.1038/s41420-025-02478-w.Peer-Reviewed Original ResearchCRC cell proliferationCircular RNAsCompetitive endogenous RNAColorectal cancer tissuesInhibited CRC cell proliferationColorectal cancer progressionRapamycin resistanceColorectal cancerEndogenous RNADrug resistancePhosphorylation of MycRNA-binding proteinsModulating CRC progressionRate of drug resistanceActivation of mTOR signalingCell proliferationAssociated with patient survivalPre-mRNACircRNAsQKI expressionMYC phosphorylationIntron 1MYC pathwayCRC progressionInduce apoptosis
2024
Regulated circRNA nuclear export in neuronal differentiation
Li D, Huang Y. Regulated circRNA nuclear export in neuronal differentiation. Trends In Cell Biology 2024, 34: 620-621. PMID: 38964955, PMCID: PMC11316627, DOI: 10.1016/j.tcb.2024.06.005.Peer-Reviewed Original ResearchDecoding protein binding landscape on circular RNAs with base-resolution transformer models
Wu H, Liu X, Fang Y, Yang Y, Huang Y, Pan X, Shen H. Decoding protein binding landscape on circular RNAs with base-resolution transformer models. Computers In Biology And Medicine 2024, 171: 108175. PMID: 38402841, DOI: 10.1016/j.compbiomed.2024.108175.Peer-Reviewed Original ResearchConceptsRNA-binding protein binding sitesRNA-binding proteinsCircRNA transcriptsBinding sitesBinding to RNA-binding proteinsSingle-nucleotide resolutionCovalent loop structureCircular RNAsBound nucleotideBinding motifBinding landscapeGene expressionTranscriptionRNANucleotideLoop structureCircRNAsProteinEndogenous RNAFragmentsSitesComputational methodsMotifGenesConvolutional neural network
2023
Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease
Dong X, Bai Y, Liao Z, Gritsch D, Liu X, Wang T, Borges-Monroy R, Ehrlich A, Serrano G, Feany M, Beach T, Scherzer C. Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease. Nature Communications 2023, 14: 5327. PMID: 37723137, PMCID: PMC10507039, DOI: 10.1038/s41467-023-40348-0.Peer-Reviewed Original ResearchConceptsAlzheimer Disease-associated geneNon-neuronal cellsDisease-associated genesCircular RNAsNeuronal identityDisease neuropathologyAutism-associated genesParkinsonism genesHuman neuropsychiatric diseasesCell identityParkinson's disease neuropathologyGenesNeuropsychiatric diseasesRNALaser captureHuman brainIdentity of dopamineCircRNAsCellsPyramidal neuronsBrain cellsSynaptic specializationsDopamine neuronsDopamineNeuronsFUS Alters circRNA Metabolism in Human Motor Neurons Carrying the ALS-Linked P525L Mutation
Colantoni A, Capauto D, Alfano V, D’Ambra E, D’Uva S, Tartaglia G, Morlando M. FUS Alters circRNA Metabolism in Human Motor Neurons Carrying the ALS-Linked P525L Mutation. International Journal Of Molecular Sciences 2023, 24: 3181. PMID: 36834591, PMCID: PMC9968238, DOI: 10.3390/ijms24043181.Peer-Reviewed Original ResearchConceptsRNA metabolismHuman motor neuronsNuclear/cytoplasmic partitioningNon-canonical splicing eventsAspects of RNASubset of circRNAsCytoplasmic partitioningCytoplasmic circRNAsSplicing eventsMutant proteinsCircular RNAsMotor neuronsAlu repeatsExon compositionCircRNAsProteinRNAMutationsFUS mutationsKey eventsFUSPreferential bindingP525L mutationMetabolismPivotal role
2022
circCsnk1g3- and circAnkib1-regulated interferon responses in sarcoma promote tumorigenesis by shaping the immune microenvironment
Piras R, Ko E, Barrett C, De Simone M, Lin X, Broz M, Tessaro F, Castillo-Martin M, Cordon-Cardo C, Goodridge H, Di Vizio D, Batish M, Lawrenson K, Chen Y, Chan K, Guarnerio J. circCsnk1g3- and circAnkib1-regulated interferon responses in sarcoma promote tumorigenesis by shaping the immune microenvironment. Nature Communications 2022, 13: 7243. PMID: 36433954, PMCID: PMC9700836, DOI: 10.1038/s41467-022-34872-8.Peer-Reviewed Original ResearchConceptsNon-coding RNA speciesExonic circular RNAsViral RNA sensorsRNA speciesInterferon-related genesSpecific circRNAsCircular RNAsSarcoma cellsCircRNAsRNA sensorsCancer progressionFunctional contributionInterferon responseSoft tissue sarcoma cellsImmune cell recruitmentPro-tumorigenic microenvironmentCellsTumor growthSarcoma growthTumor cellsPro-inflammatory elementsCell recruitmentActivationPro-inflammatory factorsMicroenvironmentHsa_Circ_0066351 Acts as a Prognostic and Immunotherapeutic Biomarker in Colorectal Cancer
Gao Y, Zhou Y, Wei L, Feng Z, Chen Y, Liu P, Peng Y, Huang Q, Gao L, Liu Y, Han Y, Shen H, Cai C, Zeng S. Hsa_Circ_0066351 Acts as a Prognostic and Immunotherapeutic Biomarker in Colorectal Cancer. Frontiers In Immunology 2022, 13: 927811. PMID: 36405685, PMCID: PMC9667793, DOI: 10.3389/fimmu.2022.927811.Peer-Reviewed Original ResearchConceptsCircRNA-miRNA-mRNA networkInhibited CRC cell proliferationCircRNA-miRNA-mRNACRC cell proliferationNon-coding RNAsEndogenous RNAInhibit CRC proliferationCircular RNAsColorectal cancerCRC proliferationColorectal cancer tissuesRNA-seq levelCell linesImmunotherapeutic biomarkersNovel classCircRNA-seqTumor suppressive functionCircRNA profilesCircRNAsQuantitative real-time PCRAssociated with better survivalColorectal cancer cell linesAssociated with distant metastasisDownstream genesReal-time PCRA bidirectional competitive interaction between circHomer1 and Homer1b within the orbitofrontal cortex regulates reversal learning
Hafez A, Zimmerman A, Papageorgiou G, Chandrasekaran J, Amoah S, Lin R, Lozano E, Pierotti C, Dell'Orco M, Hartley B, Alural B, Lalonde J, Esposito J, Berretta S, Squassina A, Chillotti C, Voloudakis G, Shao Z, Fullard J, Brennand K, Turecki G, Roussos P, Perlis R, Haggarty S, Perrone-Bizzozero N, Brigman J, Mellios N. A bidirectional competitive interaction between circHomer1 and Homer1b within the orbitofrontal cortex regulates reversal learning. Cell Reports 2022, 38: 110282. PMID: 35045295, PMCID: PMC8809079, DOI: 10.1016/j.celrep.2021.110282.Peer-Reviewed Original ResearchConceptsImportance of circRNAsRNA-binding proteinSynaptic gene expressionCircular RNAsGene expressionOrbitofrontal cortexCompetitive interactionsComplete rescuePsychiatric disordersKnockdownSynaptic expressionMechanistic insightsBrain functionMRNAHomer1bBehavioral flexibilityNeuronal culturesExpressionBiogenesisCircRNAsRNAProteinRegulatesReversal learningDisorders
2020
One Ring to Rule Them All: Mitochondrial Circular RNAs Control Mitochondrial Function
Yan L, Chen YG. One Ring to Rule Them All: Mitochondrial Circular RNAs Control Mitochondrial Function. Cell 2020, 183: 11-13. PMID: 33007261, PMCID: PMC12135702, DOI: 10.1016/j.cell.2020.09.028.Commentaries, Editorials and LettersCircular RNAs in Immune Response and Viral Infection
Yan L, Chen YG. Circular RNAs in Immune Response and Viral Infection. Trends In Biochemical Sciences 2020, 45: 1022-1034. PMID: 32900574, PMCID: PMC7642119, DOI: 10.1016/j.tibs.2020.08.006.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsCircular RNAsImmune responseDifferent biological rolesCellular abundanceViral circRNAsCircRNAs expressionBiological functionsBiological roleCircRNAsDNA virusesAutoimmune disordersImmune regulationDiverse classViral infectionClass of moleculesImmune systemRNACurrent understandingPotential roleInfectionEukaryotesFuture investigationsA psychiatric disease-related circular RNA controls synaptic gene expression and cognition
Zimmerman AJ, Hafez AK, Amoah SK, Rodriguez BA, Dell’Orco M, Lozano E, Hartley BJ, Alural B, Lalonde J, Chander P, Webster MJ, Perlis RH, Brennand KJ, Haggarty SJ, Weick J, Perrone-Bizzozero N, Brigman JL, Mellios N. A psychiatric disease-related circular RNA controls synaptic gene expression and cognition. Molecular Psychiatry 2020, 25: 2712-2727. PMID: 31988434, PMCID: PMC7577899, DOI: 10.1038/s41380-020-0653-4.Peer-Reviewed Original ResearchConceptsSynaptic gene expressionCircular RNAsGene expressionAlternative mRNA transcriptsDisease-associated circRNAsHomolog 1Neuronal RNAMRNA transcriptsRNASynaptic expressionAge of onsetMammalian brainCircRNAsPotential involvementDorsolateral prefrontal cortexOrbitofrontal cortexBipolar disorderPrefrontal cortexKnockdownExpressionFrontal cortexSynaptic plasticityNeuronal culturesPsychiatric diseasesMouse orbitofrontal cortex
2019
Exploring the Regulatory Role of Circular RNAs in Neurodegenerative Disorders
D’Ambra E, Capauto D, Morlando M. Exploring the Regulatory Role of Circular RNAs in Neurodegenerative Disorders. International Journal Of Molecular Sciences 2019, 20: 5477. PMID: 31689888, PMCID: PMC6862314, DOI: 10.3390/ijms20215477.Peer-Reviewed Original ResearchConceptsCircular RNAsRegulatory non-coding RNAsNon-coding RNAsImportant regulatory functionsNeuronal specificationPathological conditionsCircRNAs expressionGene expressionCircRNAsNeuronal developmentRegulatory functionsExact functionRegulatory roleDifferent tissuesSynaptic plasticity inductionRNANervous systemNeurodegenerative diseasesNeurodegenerative disordersInnovative therapeutic approachesDynamic modulationRecent studiesExpressionDistinctive classCurrent advancesCharacterization of Circular RNA and microRNA Profiles in Septic Myocardial Depression: a Lipopolysaccharide-Induced Rat Septic Shock Model
Zhang TN, Yang N, Goodwin JE, Mahrer K, Li D, Xia J, Wen R, Zhou H, Zhang T, Song WL, Liu CF. Characterization of Circular RNA and microRNA Profiles in Septic Myocardial Depression: a Lipopolysaccharide-Induced Rat Septic Shock Model. Inflammation 2019, 42: 1990-2002. PMID: 31332662, DOI: 10.1007/s10753-019-01060-8.Peer-Reviewed Original ResearchConceptsCircular RNAsDifferential expressionGene Ontology term enrichmentFeatures of circRNAsMiRNA-mRNA networkMicroRNA profilesBasic molecular mechanismsNovel miRNAsCellular functionsRegulatory networksTerm enrichmentRNA sequencingBioinformatics analysisComprehensive circRNARegulator networkRegulatory relationshipsMolecular mechanismsCircRNAsMetabolic processesMiRNAsHeart tissueBiological mechanismsMiRNARNAPathological processes
2018
TWIST1 regulation of circRNA: a novel mechanism to promote epithelial-mesenchymal transition in hepatocellular carcinoma
Yochum Z, Burns T. TWIST1 regulation of circRNA: a novel mechanism to promote epithelial-mesenchymal transition in hepatocellular carcinoma. Non-coding RNA Investigation 2018, 2: 71-71. PMID: 30734026, PMCID: PMC6363344, DOI: 10.21037/ncri.2018.12.01.Peer-Reviewed Original ResearchEpithelial-mesenchymal transitionCell-extracellular matrix interactionsApical-basal polarityCell-cell interactionsEpithelial cellsGenetic changesMesenchymal morphologyMatrix interactionsNovel mechanismProtein 1E-cadherinFibroblast-specific protein-1GenesCellsCircRNAsRegulationUpregulationInteractionVimentin
2017
Sensing Self and Foreign Circular RNAs by Intron Identity
Chen YG, Kim MV, Chen X, Batista PJ, Aoyama S, Wilusz JE, Iwasaki A, Chang HY. Sensing Self and Foreign Circular RNAs by Intron Identity. Molecular Cell 2017, 67: 228-238.e5. PMID: 28625551, PMCID: PMC5610545, DOI: 10.1016/j.molcel.2017.05.022.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceDEAD Box Protein 58Encephalitis Virus, Venezuelan EquineEncephalomyelitis, Venezuelan EquineHEK293 CellsHeLa CellsHost-Pathogen InteractionsHumansImmune ToleranceImmunity, InnateIntronsMiceNucleic Acid ConformationProtein BindingRAW 264.7 CellsReceptors, ImmunologicRNARNA Processing, Post-TranscriptionalRNA-Binding ProteinsRNA, CircularRNA, MessengerSpliceosomesTransfectionConceptsCircular RNAsInnate immunity genesMammalian transcriptionDiverse RNACytoplasmic fociHuman circRNAsMammalian cellsImmunity genesEndogenous splicingHuman intronsInnate immune sensingPrimary sequenceCircRNA sequenceRNA structureCircRNAsUnknown functionIntronsRNASensor RIGImmune sensingInnate immunitySelf-nonself discriminationPotent inductionSequenceBiogenesisFUS affects circular RNA expression in murine embryonic stem cell-derived motor neurons
Errichelli L, Dini Modigliani S, Laneve P, Colantoni A, Legnini I, Capauto D, Rosa A, De Santis R, Scarfò R, Peruzzi G, Lu L, Caffarelli E, Shneider NA, Morlando M, Bozzoni I. FUS affects circular RNA expression in murine embryonic stem cell-derived motor neurons. Nature Communications 2017, 8: 14741. PMID: 28358055, PMCID: PMC5379105, DOI: 10.1038/ncomms14741.Peer-Reviewed Original ResearchConceptsMouse motor neuronsCircRNA biogenesisRNA-binding protein FUSEmbryonic stem cell-derived motor neuronsCircular RNA productionRNA biosynthetic processesCircular RNA expressionStem cell-derived motor neuronsCell-derived motor neuronsAmyotrophic lateral sclerosisMost circRNAsFUS mutantsSplicing junctionsProtein FUSSplicing reactionBiosynthetic processesRNA productionToxic gainCircRNAsMotor neuronsBiogenesisRNA expressionFunction activityNuclear levelsFUS
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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