2021
Genome-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
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 fertilityPiwi maintains germline stem cells and oogenesis in Drosophila through negative regulation of Polycomb group proteins
Peng JC, Valouev A, Liu N, Lin H. Piwi maintains germline stem cells and oogenesis in Drosophila through negative regulation of Polycomb group proteins. Nature Genetics 2016, 48: 283-291. PMID: 26780607, PMCID: PMC4767590, DOI: 10.1038/ng.3486.Peer-Reviewed Original Research
2015
Piwi Is a Key Regulator of Both Somatic and Germline Stem Cells in the Drosophila Testis
Gonzalez J, Qi H, Liu N, Lin H. Piwi Is a Key Regulator of Both Somatic and Germline Stem Cells in the Drosophila Testis. Cell Reports 2015, 12: 150-161. PMID: 26119740, PMCID: PMC4497877, DOI: 10.1016/j.celrep.2015.06.004.Peer-Reviewed Original ResearchConceptsGermline stem cellsDrosophila testisSomatic cyst cellsPIWI-piRNA pathwayStem cell maintenanceCell-autonomous functionStem cellsGerm cell differentiationStem cell typesFasciclin 3GSC daughtersGermline functionSomatic rolePiwi expressionCyst cellsCell maintenanceEpigenetic mechanismsPiwiGenes keyNuclear localizationKey regulatorMolecular mechanismsCell differentiationGonadal developmentCell typesReassessment of Piwi Binding to the Genome and Piwi Impact on RNA Polymerase II Distribution
Lin H, Chen M, Kundaje A, Valouev A, Yin H, Liu N, Neuenkirchen N, Zhong M, Snyder M. Reassessment of Piwi Binding to the Genome and Piwi Impact on RNA Polymerase II Distribution. Developmental Cell 2015, 32: 772-774. PMID: 25805139, PMCID: PMC4472434, DOI: 10.1016/j.devcel.2015.03.004.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArgonaute ProteinsBase SequenceBinding SitesChromatin ImmunoprecipitationChromobox Protein Homolog 5Chromosomal Proteins, Non-HistoneDNA-Binding ProteinsDrosophila melanogasterDrosophila ProteinsGenomeHigh-Throughput Nucleotide SequencingHistone MethyltransferasesHistone-Lysine N-MethyltransferaseMethyltransferasesRNA InterferenceRNA Polymerase IIRNA, Small InterferingSequence Analysis, DNAConceptsRNA polymerase II distributionGenomic targetsHeterochromatin protein 1aRNA polymerase IICurrent bioinformatics methodsPiwi mutantsDrosophila PiwiPolymerase IIDevelopmental cellsPericentric regionsHistone methyltransferaseBioinformatics methodsBioinformatics pipelineProtein 1APiwiGenomePiRNAsEuchromatinMutantsMethyltransferaseSites
2014
PIWI proteins and PIWI-interacting RNAs in the soma
Ross RJ, Weiner MM, Lin H. PIWI proteins and PIWI-interacting RNAs in the soma. Nature 2014, 505: 353-359. PMID: 24429634, PMCID: PMC4265809, DOI: 10.1038/nature12987.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArgonaute ProteinsCiliophoraDrosophila melanogasterDrosophila ProteinsEpigenesis, GeneticFemaleGenomeHumansNeoplasmsOvaryPhenotypeRNA, Small InterferingConceptsPIWI-interacting RNAsPIWI proteinsPIWI-piRNA pathwayDiscovery of millionsWhole-body regenerationStem cell functionSomatic functionsDiverse organismsLower eukaryotesGenome rearrangementsSomatic cellsEpigenetic programmingBiological rolePathwayRNAProteinRecent studiesEukaryotesTransposonOrganismsBiologyUnanticipated dimensionsFunctionCellsRearrangement
2013
PIWI proteins are essential for early Drosophila embryogenesis
Mani SR, Megosh H, Lin H. PIWI proteins are essential for early Drosophila embryogenesis. Developmental Biology 2013, 385: 340-349. PMID: 24184635, PMCID: PMC3915879, DOI: 10.1016/j.ydbio.2013.10.017.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArgonaute ProteinsDrosophila melanogasterDrosophila ProteinsEmbryonic DevelopmentConceptsPIWI proteinsMitotic defectsEarly embryogenesisArgonaute/PIWI protein familySmall non-coding RNAsEarly Drosophila embryogenesisAsynchronous nuclear divisionPosttranscriptional gene regulationSevere mitotic defectsPIWI protein familyNon-coding RNAsCell cycle progressionCell cycle arrestGermline developmentDrosophila embryogenesisChromatin structureGene regulationSyncytial embryosMitotic machinerySomatic nucleiProtein familyPiwiNuclear divisionNuclear migrationEssential functionsChromatin Immunoprecipitation Assay of Piwi in Drosophila
Yin H, Lin H. Chromatin Immunoprecipitation Assay of Piwi in Drosophila. Methods In Molecular Biology 2013, 1093: 1-11. PMID: 24178552, DOI: 10.1007/978-1-62703-694-8_1.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArgonaute ProteinsCell NucleusChromatin ImmunoprecipitationDrosophila melanogasterDrosophila ProteinsFemaleGenomicsConceptsSmall RNA pathwaysRNA pathwaysArgonaute protein familyChromatin-associated factorsChromatin immunoprecipitation methodChromatin immunoprecipitation assaysWhole-genome mappingArgonaute proteinsDrosophila PiwiEpigenetic regulationDevelopmental biologyProtein familyImmunoprecipitation assaysCell biologyImmunoprecipitation methodHigh-resolution mapsPiwiEffector componentsBiologyPathwayGeneral utilityDrosophilaEpigenomeBiogenesisEpigeneticsFunction 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
A High-Resolution Whole-Genome Map of Key Chromatin Modifications in the Adult Drosophila melanogaster
Yin H, Sweeney S, Raha D, Snyder M, Lin H. A High-Resolution Whole-Genome Map of Key Chromatin Modifications in the Adult Drosophila melanogaster. PLOS Genetics 2011, 7: e1002380. PMID: 22194694, PMCID: PMC3240582, DOI: 10.1371/journal.pgen.1002380.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChromatin Assembly and DisassemblyChromatin ImmunoprecipitationChromosomal Proteins, Non-HistoneChromosome MappingDrosophila melanogasterDrosophila ProteinsEpigenesis, GeneticEuchromatinGenome, InsectHeterochromatinHigh-Throughput Nucleotide SequencingHistonesRepetitive Sequences, Nucleic AcidRetroelementsRNA Polymerase IITranscription Initiation SiteConceptsHeterochromatin protein 1aChromatin modificationsStart siteChromatin modification landscapeKey chromatin modificationKey histone marksCell typesDrosophila cell typesRNA polymerase IIAdult Drosophila melanogasterTranscriptional start siteDiverse cell typesTranscription start siteFunctionality of genesHigh-Resolution WholeEuchromatic marksHistone codeHistone marksModification landscapeDrosophila melanogasterPolymerase IIGenome mapChromatin immunoprecipitationRegulatory sequencesSplicing junctionsPAPI, 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
2009
The Yb protein defines a novel organelle and regulates male germline stem cell self-renewal in Drosophila melanogaster
Szakmary A, Reedy M, Qi H, Lin H. The Yb protein defines a novel organelle and regulates male germline stem cell self-renewal in Drosophila melanogaster. Journal Of Cell Biology 2009, 185: 613-627. PMID: 19433453, PMCID: PMC2711570, DOI: 10.1083/jcb.200903034.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell DivisionDrosophila melanogasterDrosophila ProteinsFemaleGerm CellsMaleOrganellesOvaryStem CellsTestisConceptsYB proteinsNiche cellsYb bodiesElectron-dense spheresDrosophila melanogasterGermline stem cell maintenanceMale germline stem cellsGermline stem cellsStem cell maintenanceStem cellsC-terminal regionSomatic stem cellsN-terminal regionD. melanogasterNovel organellePiwi expressionGermline cellsDouble mutantCell maintenanceNovel lociSomatic cellsCytoplasmic spotsMelanogasterCytoplasmic structuresGermline loss
2007
An epigenetic activation role of Piwi and a Piwi-associated piRNA in Drosophila melanogaster
Yin H, Lin H. An epigenetic activation role of Piwi and a Piwi-associated piRNA in Drosophila melanogaster. Nature 2007, 450: 304-308. PMID: 17952056, DOI: 10.1038/nature06263.Peer-Reviewed Original ResearchDrosophila PIWI associates with chromatin and interacts directly with HP1a
Brower-Toland B, Findley SD, Jiang L, Liu L, Yin H, Dus M, Zhou P, Elgin SC, Lin H. Drosophila PIWI associates with chromatin and interacts directly with HP1a. Genes & Development 2007, 21: 2300-2311. PMID: 17875665, PMCID: PMC1973144, DOI: 10.1101/gad.1564307.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAnimalsArgonaute ProteinsBinding SitesChromatinChromobox Protein Homolog 5Chromosomal Proteins, Non-HistoneDrosophila melanogasterDrosophila ProteinsEmbryo, NonmammalianFemaleGene SilencingMaleModels, MolecularNuclear ProteinsProtein BindingProteinsRNA-Induced Silencing ComplexConceptsHeterochromatin protein 1aPIWI-interacting RNAsEpigenetic changesChromatin-associated proteinsProtein family membersNormal silencingHeterochromatic genesFly genomeHeterochromatin componentsChromatin modifiersEpigenetic stateEpigenetic regulationRNA mechanismFruit flyPiwiTerminal domainProtein 1ACentral playerRNASpecific sequencesDirect interactionGenomeGenesMotifCellular systems