2022
Identification and functional implications of pseudouridine RNA modification on small noncoding RNAs in the mammalian pathogen Trypanosoma brucei
Rajan KS, Adler K, Doniger T, Cohen-Chalamish S, Aharon-Hefetz N, Aryal S, Pilpel Y, Tschudi C, Unger R, Michaeli S. Identification and functional implications of pseudouridine RNA modification on small noncoding RNAs in the mammalian pathogen Trypanosoma brucei. Journal Of Biological Chemistry 2022, 298: 102141. PMID: 35714765, PMCID: PMC9283944, DOI: 10.1016/j.jbc.2022.102141.Peer-Reviewed Original ResearchConceptsRNA modificationsLife stagesStage-specific regulationGenome-wide approachesSmall nucleolar RNAsΨ modificationsSmall noncoding RNAsDifferent host environmentsProtein translocationD snoRNAsRRNA modificationVault RNARRNA processingNucleolar RNAsRiboMeth-seqNoncoding RNAsMammalian hostsTrypanosoma bruceiProtein synthesisHost environmentRNAFunctional implicationsTRNABruceiParasites
2021
CPA-seq reveals small ncRNAs with methylated nucleosides and diverse termini
Wang H, Huang R, Li L, Zhu J, Li Z, Peng C, Zhuang X, Lin H, Shi S, Huang P. CPA-seq reveals small ncRNAs with methylated nucleosides and diverse termini. Cell Discovery 2021, 7: 25. PMID: 33867522, PMCID: PMC8053708, DOI: 10.1038/s41421-021-00265-2.Peer-Reviewed Original ResearchSmall noncoding RNAsMethylated nucleosidesHepatic reprogrammingPolynucleotide kinaseHigh-throughput sequencingSRNA transcriptomeTissue-specific differencesSmall ncRNAsT4 polynucleotide kinaseNoncoding RNAsAdapter ligationMouse tissuesAcid pyrophosphataseReprogrammingComplex landscapeMethylationTerminusReverse transcriptionRNASequencingMicroRNA regulation of cholesterol metabolism
Citrin KM, Fernández‐Hernando C, Suárez Y. MicroRNA regulation of cholesterol metabolism. Annals Of The New York Academy Of Sciences 2021, 1495: 55-77. PMID: 33521946, PMCID: PMC8938903, DOI: 10.1111/nyas.14566.Peer-Reviewed Original ResearchConceptsDifferent cell typesCell typesMultiple mRNA targetsCholesterol homeostasisSmall noncoding RNAsMicroRNA activityCholesterol-laden cellsMicroRNA regulationCholesterol metabolismMRNA targetsNoncoding RNAsPosttranscriptional levelGene expressionSpecialized functionsMicroRNAsCurrent knowledgeTarget interactionsHomeostasisMetabolismPathwayExpressionMultiple stagesRNARegulationDistinctive effectsRoles of piRNAs in transposon and pseudogene regulation of germline mRNAs and lncRNAs
Wang C, Lin H. Roles of piRNAs in transposon and pseudogene regulation of germline mRNAs and lncRNAs. Genome Biology 2021, 22: 27. PMID: 33419460, PMCID: PMC7792047, DOI: 10.1186/s13059-020-02221-x.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsPIWI proteinsRole of piRNAsPIWI-piRNA pathwayRNA-binding proteinSmall noncoding RNAsGermline mRNAsGermline developmentNoncoding RNAsRegulatory relationshipsGerm cellsRNAProteinTransposonMajor classesRNA levelsRecent studiesExpressionGenomeSubfamiliesGermlineLncRNAsMajor constituentsMRNARegulation
2020
Hfq and sRNA 179 Inhibit Expression of the Pseudomonas aeruginosa cAMP-Vfr and Type III Secretion Regulons
Janssen KH, Corley JM, Djapgne L, Cribbs JT, Voelker D, Slusher Z, Nordell R, Regulski EE, Kazmierczak BI, McMackin EW, Yahr TL. Hfq and sRNA 179 Inhibit Expression of the Pseudomonas aeruginosa cAMP-Vfr and Type III Secretion Regulons. MBio 2020, 11: 10.1128/mbio.00363-20. PMID: 32546612, PMCID: PMC7298702, DOI: 10.1128/mbio.00363-20.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsCyclic AMP Receptor ProteinCyclic AMP-Dependent Protein KinasesGene Expression Regulation, BacterialGene LibraryHost Factor 1 ProteinPromoter Regions, GeneticPseudomonas aeruginosaRegulonRNA, BacterialRNA, Small UntranslatedTranscription, GeneticType III Secretion SystemsVirulence FactorsConceptsSmall noncoding RNAsType III secretion systemSecretion systemNoncoding RNAsGene expressionTranscription factorsExpression libraryGac/Rsm systemType VI secretion systemT3SS gene expressionCAMP-responsive transcription factorRNA-binding proteinVirulence factorsGram-negative opportunistic pathogenRNA chaperonesGlobal regulatorT3SS regulonMutant lackingTarget mRNAsCritical virulence factorImportant virulence factorMRNA targetsHfqRegulonRsm system
2018
Region-specific microRNA signatures in the human epididymis
Browne JA, Leir SH, Eggener SE, Harris A. Region-specific microRNA signatures in the human epididymis. Asian Journal Of Andrology 2018, 20: 539-544. PMID: 30058558, PMCID: PMC6219309, DOI: 10.4103/aja.aja_40_18.Peer-Reviewed Original ResearchConceptsGene expressionSegment-specific gene expressionImportant gene networksRegionalized expression patternsRegionalized gene expressionGene ontology pathwaysSmall noncoding RNAsHuman epididymisEpithelial cellsOntology pathwaysGene networksNoncoding RNAsTarget genesHuman epididymal tissueExpression patternsSperm maturationMiR-573MiRNA expressionMiRNAsDifferentiated functionsMicroRNAsMicroRNA profilesMale fertilityLuminal environmentMiRNA signatureA critical role for nucleoporin 358 (Nup358) in transposon silencing and piRNA biogenesis in Drosophila
Parikh RY, Lin H, Gangaraju VK. A critical role for nucleoporin 358 (Nup358) in transposon silencing and piRNA biogenesis in Drosophila. Journal Of Biological Chemistry 2018, 293: 9140-9147. PMID: 29735528, PMCID: PMC6005430, DOI: 10.1074/jbc.ac118.003264.Peer-Reviewed Original ResearchMeSH KeywordsActive Transport, Cell NucleusAnimalsArgonaute ProteinsDNA Transposable ElementsDrosophilaDrosophila ProteinsFemaleGene Expression RegulationGene SilencingGenomic InstabilityGerm CellsMaleMolecular ChaperonesNuclear Pore Complex ProteinsProtein Interaction MapsRNA, Small InterferingTranscription, GeneticConceptsPIWI-interacting RNAsPing-pong cycleNuclear pore complexPiRNA biogenesisGermline knockdownPiRNA pathwayAntisense Piwi-interacting RNAsPiRNA precursor transcriptionSmall noncoding RNAsPiwi functionSilence transposonsPIWI proteinsShort hairpin RNACritical roleArgonaute 3Pore complexNoncoding RNAsGenomic instabilityNuclear localizationGene expressionTransposonNup358Germ cellsBiogenesisHairpin RNA
2017
Chapter 15 Comparative Functions of miRNAs in Embryonic Neurogenesis and Neuronal Network Formation
Ristori E, Nicoli S. Chapter 15 Comparative Functions of miRNAs in Embryonic Neurogenesis and Neuronal Network Formation. 2017, 265-282. DOI: 10.1016/b978-0-12-804402-5.00015-7.Peer-Reviewed Original ResearchTarget mRNA degradationCell fate determinationGene regulatory pathwaysDynamic spatiotemporal expressionImportance of miRNAsSmall noncoding RNAsStem cell proliferationMulticellular organismsFate determinationMost miRNAsNeuronal network formationTranslational repressionModel organismsNeural stem cell proliferationMRNA degradationPosttranscriptional regulatorsNoncoding RNAsRegulatory pathwaysDevelopmental processesEmbryonic neurogenesisGene expressionSpatiotemporal expressionNovel roleNeuronal differentiationMiRNAs
2015
Splicing remodels the let-7 primary microRNA to facilitate Drosha processing in Caenorhabditis elegans
Mondol V, Ahn B, Pasquinelli A. Splicing remodels the let-7 primary microRNA to facilitate Drosha processing in Caenorhabditis elegans. RNA 2015, 21: 1396-1403. PMID: 26081559, PMCID: PMC4509930, DOI: 10.1261/rna.052118.115.Peer-Reviewed Original ResearchConceptsPri-let-7Spliced leader 1Caenorhabditis elegansBiogenesis of let-7 miRNAsSecondary structureRNA secondary structureLet-7Partial base-pairingMature let-7Messenger RNASmall noncoding RNAsLet-7 miRNAsTransgenic worm strainsTrans-splicingSplicing eventsSplice sitePri-miRNAsPrimary microRNAsMicroprocessor complexBase pairsPre-miRNAsPrecursor miRNAsProcessing eventsSplicingMature miRNAsViral noncoding RNAs: more surprises
Tycowski KT, Guo YE, Lee N, Moss WN, Vallery TK, Xie M, Steitz JA. Viral noncoding RNAs: more surprises. Genes & Development 2015, 29: 567-584. PMID: 25792595, PMCID: PMC4378190, DOI: 10.1101/gad.259077.115.Peer-Reviewed Original ResearchConceptsDiverse biological rolesSmall noncoding RNAsMultitude of functionsHost immune evasionEukaryotic cellsCellular transformationNoncoding RNAsHost counterpartsAnimal virusesBiological roleNcRNAsRNA virusesViral ncRNAsMechanism of actionImmune evasionViral replicationMore surprisesBiogenesisViral persistenceRNAProteinDNAVirusRegulationReplicationmicroRNA Expression Profiling: Technologies, Insights, and Prospects
Roden C, Mastriano S, Wang N, Lu J. microRNA Expression Profiling: Technologies, Insights, and Prospects. Advances In Experimental Medicine And Biology 2015, 888: 409-421. PMID: 26663195, DOI: 10.1007/978-3-319-22671-2_21.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCell Line, TumorDisease Models, AnimalGene Expression ProfilingGene Expression Regulation, NeoplasticHigh-Throughput Nucleotide SequencingHumansMicroRNAsMolecular Sequence DataNeoplasmsReverse Transcriptase Polymerase Chain ReactionSequence Homology, Nucleic AcidSignal TransductionConceptsLong small noncoding RNAsExpression profilingMiRNA isoformsMiRNA expressionProfiling technologiesDiverse biological processesSingle-cell variabilitySmall noncoding RNAsMiRNA profiling technologiesGlobal miRNA expressionNext-generation sequencingNoncoding RNAsCell variabilitySingle-molecule measurementsBiological functionsBiological processesTumor suppressorMicroRNA researchQuantitative RT-PCRCareful experimental designMiRNAsIsoformsRT-PCRProfilingExpression
2014
The Coilin Interactome Identifies Hundreds of Small Noncoding RNAs that Traffic through Cajal Bodies
Machyna M, Kehr S, Straube K, Kappei D, Buchholz F, Butter F, Ule J, Hertel J, Stadler PF, Neugebauer KM. The Coilin Interactome Identifies Hundreds of Small Noncoding RNAs that Traffic through Cajal Bodies. Molecular Cell 2014, 56: 389-399. PMID: 25514182, DOI: 10.1016/j.molcel.2014.10.004.Peer-Reviewed Original ResearchConceptsCajal bodiesSmall nucleolar RNAsSmall nuclear RNASmall noncoding RNAsChIP-seq peaksCoilin proteinSnoRNA biogenesisRNP assemblySnRNP assemblyNcRNA metabolismSnRNA genesSubnuclear compartmentsCellular hubHuman snoRNAsMolecular functionsSnRNA transcriptsNucleolar RNAsNoncoding RNAsNuclear RNACoilinRNASignal trafficRole of CBAssemblySnRNAsmiRNAs Expression Profile in Zebrafish Developing Vessels
Ristori E, Nicoli S. miRNAs Expression Profile in Zebrafish Developing Vessels. Methods In Molecular Biology 2014, 1214: 129-150. PMID: 25468601, DOI: 10.1007/978-1-4939-1462-3_7.Peer-Reviewed Original ResearchConceptsExpression profilesZebrafish embryonic developmentSmall RNA librariesSmall noncoding RNAsDeep sequencing strategyQuantification of miRNAsPrimary endothelial cellsMiRNAs expression profilesRNA librariesNovel miRNAEmbryonic developmentNoncoding RNAsEndothelial cellsRNA strategySequence variantsSequencing strategyMiRNAsRNACellsMiRNAEarly stagesFACSAngiogenesisVariantsVirus Meets Host MicroRNA: the Destroyer, the Booster, the Hijacker
Guo YE, Steitz JA. Virus Meets Host MicroRNA: the Destroyer, the Booster, the Hijacker. Molecular And Cellular Biology 2014, 34: 3780-3787. PMID: 25047834, PMCID: PMC4187717, DOI: 10.1128/mcb.00871-14.Peer-Reviewed Original ResearchConceptsKey regulatory stepSmall noncoding RNAsVirus-host interactionsViral life cycleNoncoding RNAsCellular miRNAsMiRNA interactionsRegulatory stepGene expressionProtein productionHost microRNAsRNA virusesRecent discoveryLife cycleMicroRNAsMiRNAsRNADNAMRNAVirusExpressionInteractionMinireviewDiscoveryA High-Throughput MicroRNA Expression Profiling System
Guo Y, Mastriano S, Lu J. A High-Throughput MicroRNA Expression Profiling System. Methods In Molecular Biology 2014, 1176: 33-44. PMID: 25030917, DOI: 10.1007/978-1-4939-0992-6_4.Peer-Reviewed Original ResearchConceptsHundreds of miRNAsSmall noncoding RNAsDiverse biological functionsMiRNA-related researchGlobal miRNA expressionTotal RNA samplesNoncoding RNAsBiological functionsHundreds of samplesMiRNA expressionRNA samplesMiRNA levelsBiochemical reactionsPathological processesRobust protocolBead-based detectionExpressionLarge numberMiRNAsMicroRNAsHigh detection specificityRNADetection specificityDeregulationHundreds
2013
MicroRNA 33 Regulates Glucose Metabolism
Ramírez CM, Goedeke L, Rotllan N, Yoon JH, Cirera-Salinas D, Mattison JA, Suárez Y, de Cabo R, Gorospe M, Fernández-Hernando C. MicroRNA 33 Regulates Glucose Metabolism. Molecular And Cellular Biology 2013, 33: 2891-2902. PMID: 23716591, PMCID: PMC3719675, DOI: 10.1128/mcb.00016-13.Peer-Reviewed Original ResearchConceptsHost genesSterol regulatory element-binding protein (SREBP) genesSmall noncoding RNAsKey regulatory enzymeMiR-33bIntronic miRNAsHuman hepatic cellsMiR-33a/bPosttranscriptional regulationRegulatory genesExpression of PCK1Regulation of lipidNoncoding RNAsProtein geneG6pc expressionGene expressionBiological processesRegulatory enzymeMicroRNA-33GenesSpecific pathwaysMetabolic diseasesNovel therapeutic targetPhosphoenolpyruvate carboxykinaseRecent discovery
2011
High Throughput Sequencing Following Cross-Linked Immune Precipitation (HITS-CLIP) of Argonaute (AGO) Identifies Mir-9 As a Regulator of MMP2 in the Marrow Microenvironment (ME)
Balakrishnan I, Yang X, Torok-Storb B, Hesselberth J, Pillai M. High Throughput Sequencing Following Cross-Linked Immune Precipitation (HITS-CLIP) of Argonaute (AGO) Identifies Mir-9 As a Regulator of MMP2 in the Marrow Microenvironment (ME). Blood 2011, 118: 2392. DOI: 10.1182/blood.v118.21.2392.2392.Peer-Reviewed Original ResearchGenome-wide approachesHITS-CLIPMiRNA-mRNA interactomeMiR-9Functional nichesNext-generation sequencingHuman umbilical vein endothelial cellsGene expressionMarrow microenvironmentNew genome-wide approachDirect bindingLuciferase assayMiRNA-based regulationPost-transcriptional regulationCross-species conservationSpecific functional nichesHigh-throughput sequencingMiRNA-mRNA interactionsSmall noncoding RNAsRegulation of hematopoiesisPutative binding sitesStromal cellsCobblestone areaSequence-specific fashionCross-linked RNASmall Noncoding RNAs in the Germline
Saxe JP, Lin H. Small Noncoding RNAs in the Germline. Cold Spring Harbor Perspectives In Biology 2011, 3: a002717. PMID: 21669983, PMCID: PMC3181032, DOI: 10.1101/cshperspect.a002717.Peer-Reviewed Original ResearchConceptsRNA pathwaysSmall noncoding RNAsTarget mRNAsNoncoding RNAsSmall RNA pathwaysPiRNA pathwayGermline specificationMicroRNA pathwayMiRNA pathwayGene regulationMRNA translationSomatic tissuesEpigenetic programmingDiverse functionsGene expressionRegulatory functionsGermlinePotent regulatorPathwayRNAMRNARegulationPiwiBiogenesisTransposon
2009
The Biogenesis and Function of PIWI Proteins and piRNAs: Progress and Prospect
Thomson T, Lin H. The Biogenesis and Function of PIWI Proteins and piRNAs: Progress and Prospect. Annual Review Of Cell And Developmental Biology 2009, 25: 355-376. PMID: 19575643, PMCID: PMC2780330, DOI: 10.1146/annurev.cellbio.24.110707.175327.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsPIWI proteinsGermline stem cell maintenanceStem cell maintenanceSmall noncoding RNAsGermline determinationAGO proteinsGermline developmentMetazoan speciesPiRNA speciesPIWI subfamiliesSmall RNAsIntergenic sequencesPosttranscriptional regulationCell maintenanceRNA precursorsNoncoding RNAsPiwi familyDiverse functionsDiverse tissuesRNANovel mechanismProteinBiogenesisSpeciesMili Interacts with Tudor Domain-Containing Protein 1 in Regulating Spermatogenesis
Wang J, Saxe JP, Tanaka T, Chuma S, Lin H. Mili Interacts with Tudor Domain-Containing Protein 1 in Regulating Spermatogenesis. Current Biology 2009, 19: 640-644. PMID: 19345100, PMCID: PMC2704239, DOI: 10.1016/j.cub.2009.02.061.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsPiRNA biogenesisPIWI proteinsTudor domainChromatoid bodyMammalian Piwi proteinsMultiple Tudor domainsGermline-specific organelleTudor domain–containing protein-1Domain-containing protein 1RNA-independent interactionSmall noncoding RNAsProtein 1N-terminal regionGermline developmentGermline proteinsEpigenetic regulationNoncoding RNAsTerminal domainMILIRegulatory mechanismsMolecular mechanismsSpermatogenic defectsProteinBiogenesis
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