2021
Roles 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 constituentsMRNARegulationGenome-wide mapping of Piwi association with specific loci in Drosophila ovaries
Liu N, Neuenkirchen N, Zhong M, Lin H. Genome-wide mapping of Piwi association with specific loci in Drosophila ovaries. G3: Genes, Genomes, Genetics 2021, 11: jkaa059. PMID: 33609367, PMCID: PMC8022938, DOI: 10.1093/g3journal/jkaa059.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArgonaute ProteinsDNA Transposable ElementsDrosophilaDrosophila melanogasterDrosophila ProteinsEpigenesis, GeneticFemaleOvaryRNA, Small InterferingConceptsPIWI-interacting RNAsProtein-coding genesDrosophila ovaryGermline stem cell maintenanceRole of piRNAsTermination sitesGenome-wide mappingGenomic binding profileTranscriptional termination sitesSpecific genomic sitesStem cell maintenanceRNA pathwaysTransposon repressionTranscriptional startEuchromatic regionsGene regulationEpigenetic regulationGenomic sitesCell maintenancePiwiSpecific lociMethylation signalsDiverse mechanismsTarget siteBinding sites
2020
PIWI–piRNA pathway-mediated transposable element repression in Hydra somatic stem cells
Teefy BB, Siebert S, Cazet JF, Lin H, Juliano CE. PIWI–piRNA pathway-mediated transposable element repression in Hydra somatic stem cells. RNA 2020, 26: 550-563. PMID: 32075940, PMCID: PMC7161359, DOI: 10.1261/rna.072835.119.Peer-Reviewed Original ResearchConceptsPIWI-piRNA pathwayTE expressionSomatic stem cellsTransposable elementsTE transcriptsStem cellsFreshwater cnidarianSmall RNA pathwaysTransposable element repressionSomatic cell lineagesGermline of animalsInterstitial stem cellsStem cell populationInterstitial lineageSomatic piRNAsDegradome sequencingEpithelial cellsAncestral functionRNA pathwaysGermline piRNAsPIWI proteinsTE repressionGermline competenceSequence signaturesRNA immunoprecipitation
2018
A 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
2016
Tudor-SN Interacts with Piwi Antagonistically in Regulating Spermatogenesis but Synergistically in Silencing Transposons in Drosophila
Ku HY, Gangaraju VK, Qi H, Liu N, Lin H. Tudor-SN Interacts with Piwi Antagonistically in Regulating Spermatogenesis but Synergistically in Silencing Transposons in Drosophila. PLOS Genetics 2016, 12: e1005813. PMID: 26808625, PMCID: PMC4726654, DOI: 10.1371/journal.pgen.1005813.Peer-Reviewed Original ResearchConceptsPiRNA biogenesisPrimordial germ cellsPiwi expressionTudor-SNSomatic cellsGerm cellsDiverse molecular functionsPost-transcriptional regulationEmbryonic somatic cellsPiwi mutantsDosage-dependent mannerGermline developmentPIWI proteinsMutant phenotypeMeiotic cytokinesisMolecular functionsSpliceosome assemblyPiwiEpigenetic programmingDiverse functionsBiological functionsAdult ovariesBiogenesisTransposonMale fertility
2013
Beyond transposons: the epigenetic and somatic functions of the Piwi-piRNA mechanism
Peng JC, Lin H. Beyond transposons: the epigenetic and somatic functions of the Piwi-piRNA mechanism. Current Opinion In Cell Biology 2013, 25: 190-194. PMID: 23465540, PMCID: PMC3651849, DOI: 10.1016/j.ceb.2013.01.010.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArgonaute ProteinsDNA Transposable ElementsDrosophila ProteinsEpigenesis, GeneticGene SilencingHistonesRNA, Small InterferingConceptsPIWI-interacting RNAsPIWI-piRNA pathwayBiogenesis of piRNAsSmall non-coding RNAsPost-transcriptional regulationNon-coding RNAsPIWI proteinsGene regulationSomatic cellsPiwi familyGene expressionGeneral mechanismSomatic functionsTransposonPathwayRNARegulationNovel classRecent studiesBiogenesisNew findingsProteinMechanismExpressionFunctionA Major Epigenetic Programming Mechanism Guided by piRNAs
Huang XA, Yin H, Sweeney S, Raha D, Snyder M, Lin H. A Major Epigenetic Programming Mechanism Guided by piRNAs. Developmental Cell 2013, 24: 502-516. PMID: 23434410, PMCID: PMC3600162, DOI: 10.1016/j.devcel.2013.01.023.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, Genetically ModifiedArgonaute ProteinsChromatinChromatin ImmunoprecipitationChromobox Protein Homolog 5Chromosomal Proteins, Non-HistoneDNA Transposable ElementsDrosophilaDrosophila ProteinsEpigenomicsGenomeGenomicsMethyltransferasesMutationReal-Time Polymerase Chain ReactionReverse Transcriptase Polymerase Chain ReactionRNA Polymerase IIRNA, MessengerRNA, Small InterferingConceptsSpecific genomic sitesEpigenetic factorsGenomic sitesRNA polymerase II associationPiwi-piRNA complexDrosophila genomeEpigenetic stateEpigenetic landscapeComplex associatesPiwiGenomePiRNAsCentral enigmaMajor mechanismEctopic sitesSequenceHP1aDrosophilaPiRNASitesEpigeneticsMechanismProgramming mechanismAssociatesRecruitmentFunction of Piwi, a nuclear Piwi/Argonaute protein, is independent of its slicer activity
Darricarrère N, Liu N, Watanabe T, Lin H. Function of Piwi, a nuclear Piwi/Argonaute protein, is independent of its slicer activity. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 1297-1302. PMID: 23297219, PMCID: PMC3557079, DOI: 10.1073/pnas.1213283110.Peer-Reviewed Original ResearchConceptsPIWI proteinsPiRNA biogenesisSlicer activityPIWI-interacting RNA (piRNA) biogenesisEndonuclease activityFunction of PiwiNuclear Piwi proteinSecondary piRNA biogenesisGerm line developmentPiwi functionPiwi membersArgonaute proteinsRNA biogenesisArgonaute 3Transgenic fliesPiwiSomatic cellsCatalytic triadEpigenetic factorsRegulatory functionsBiogenesisOnly memberProteinTransposonRecent evidence
2011
Uniting Germline and Stem Cells: The Function of Piwi Proteins and the piRNA Pathway in Diverse Organisms
Juliano C, Wang J, Lin H. Uniting Germline and Stem Cells: The Function of Piwi Proteins and the piRNA Pathway in Diverse Organisms. Annual Review Of Genetics 2011, 45: 447-469. PMID: 21942366, PMCID: PMC3832951, DOI: 10.1146/annurev-genet-110410-132541.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsPIWI proteinsDiverse organismsStem cellsArgonaute protein familyPIWI-piRNA pathwayStem cell maintenanceSomatic stem/progenitor cellsAdult stem cellsStem/progenitor cellsPiRNA pathwayGermline specificationAnimal phylogenyGenome integrityProtein familyPosttranscriptional regulationCell maintenanceProtein bindsSomatic cellsEpigenetic programmingGermlineProgenitor cellsProteinOrganismsCommon mechanismPAPI, a novel TUDOR-domain protein, complexes with AGO3, ME31B and TRAL in the nuage to silence transposition
Liu L, Qi H, Wang J, Lin H. PAPI, a novel TUDOR-domain protein, complexes with AGO3, ME31B and TRAL in the nuage to silence transposition. Development 2011, 138: 1863-1873. PMID: 21447556, PMCID: PMC3074456, DOI: 10.1242/dev.059287.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, Genetically ModifiedArgonaute ProteinsCarrier ProteinsDEAD-box RNA HelicasesDNA Transposable ElementsDrosophila melanogasterDrosophila ProteinsEmbryo, NonmammalianFemaleGene Expression Regulation, DevelopmentalGene SilencingGerm CellsMaleModels, BiologicalMutagenesis, InsertionalPeptide Initiation FactorsProtein BindingRibonucleoproteinsRNA-Binding ProteinsRNA-Induced Silencing ComplexConceptsPiRNA pathway componentsPIWI-interacting RNAsArgonaute 3PiRNA pathwayPIWI proteinsTransposon activationPathway componentsPIWI protein AubergineTudor domain proteinsP-body componentsN-terminal domainNuage componentsPiRNA mutantsTransposon controlGermline developmentTudor domainMutant ovariesArginine methyltransferaseGermline genomeEpigenetic regulationPerinuclear structuresNuageAdult ovariesArginine residuesFunctional interaction
2010
Drosophila Piwi functions in Hsp90-mediated suppression of phenotypic variation
Gangaraju VK, Yin H, Weiner MM, Wang J, Huang XA, Lin H. Drosophila Piwi functions in Hsp90-mediated suppression of phenotypic variation. Nature Genetics 2010, 43: 153-158. PMID: 21186352, PMCID: PMC3443399, DOI: 10.1038/ng.743.Peer-Reviewed Original ResearchMeSH KeywordsAllelesAnimalsArgonaute ProteinsDNA Transposable ElementsDrosophila melanogasterDrosophila ProteinsElectrophoresis, Gel, Two-DimensionalEpigenesis, GeneticFemaleGene SilencingGenetic VariationGreen Fluorescent ProteinsHSP90 Heat-Shock ProteinsMaleOvaryPhenotypeRNA-Induced Silencing Complex