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
Piwi 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
2014
Noncoding RNAs in the regulation of DNA replication
Ge XQ, Lin H. Noncoding RNAs in the regulation of DNA replication. Trends In Biochemical Sciences 2014, 39: 341-343. PMID: 25027733, PMCID: PMC4265214, DOI: 10.1016/j.tibs.2014.06.003.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDNA ReplicationGene Expression RegulationHumansRNA, UntranslatedTranscription, Genetic
2011
Role for piRNAs and Noncoding RNA in de Novo DNA Methylation of the Imprinted Mouse Rasgrf1 Locus
Watanabe T, Tomizawa S, Mitsuya K, Totoki Y, Yamamoto Y, Kuramochi-Miyagawa S, Iida N, Hoki Y, Murphy PJ, Toyoda A, Gotoh K, Hiura H, Arima T, Fujiyama A, Sado T, Shibata T, Nakano T, Lin H, Ichiyanagi K, Soloway PD, Sasaki H. Role for piRNAs and Noncoding RNA in de Novo DNA Methylation of the Imprinted Mouse Rasgrf1 Locus. Science 2011, 332: 848-852. PMID: 21566194, PMCID: PMC3368507, DOI: 10.1126/science.1203919.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArgonaute ProteinsDNA MethylationGenomic ImprintingMaleMiceMice, Inbred C57BLMitochondrial ProteinsModels, GeneticMutationPhospholipase DProteinsRas-GRF1Repetitive Sequences, Nucleic AcidRetroelementsRNA, Small InterferingRNA, UntranslatedSpermatogoniaTestisTranscription, GeneticConceptsRasgrf1 locusDNA methylationPIWI-interacting RNA (piRNA) pathwayDe novo DNA methylationMonoallelic gene expressionNovo DNA methylationParental germ lineDe novo methylationSequence-specific methylationDifferential DNA methylationRNA pathwaysGenomic imprintingNovo methylationRetrotransposon sequencesGerm lineNoncoding RNAsGene expressionDirect repeatsPiRNAsTarget RNADifferent lociMethylationLociRNASpecific sequences
2010
Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing
Wu JQ, Habegger L, Noisa P, Szekely A, Qiu C, Hutchison S, Raha D, Egholm M, Lin H, Weissman S, Cui W, Gerstein M, Snyder M. Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proceedings Of The National Academy Of Sciences Of The United States Of America 2010, 107: 5254-5259. PMID: 20194744, PMCID: PMC2841935, DOI: 10.1073/pnas.0914114107.Peer-Reviewed Original ResearchConceptsNeural differentiationUndifferentiated hESCsNeural fate specificationCell identity maintenanceStage-specific regulationHuman embryonic stem cellsTypes of genesPaired-end sequencingDifferentiation of hESCsEmbryonic stem cellsPaired-end readsNeural cell differentiationSplicing dynamicsFate specificationDynamic transcriptomeIsoform diversityTranscriptome changesUnannotated transcriptsGene transcriptionRNA sequencingStages of differentiationNeural lineagesCell differentiationDifferential expressionGliogenic potential
2009
MicroRNAs: key regulators of stem cells
Gangaraju VK, Lin H. MicroRNAs: key regulators of stem cells. Nature Reviews Molecular Cell Biology 2009, 10: 116-125. PMID: 19165214, PMCID: PMC4118578, DOI: 10.1038/nrm2621.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsAdult tissue stem cellsStem cell processesTissue stem cellsSmall RNAsStem cellsCell processesNext-generation sequencing technologiesKey protein factorsLong non-coding RNAsNon-coding RNAsNumber of miRNAsGeneration sequencing technologyTranscriptional machineryNew miRNAsAsymmetric divisionDaughter cellsTarget mRNAsProtein factorsMaster regulatorSequencing technologiesKey regulatorUntranslated regionDifferentiation pathwayMiRNAs
2003
Screens for piwi Suppressors in Drosophila Identify Dosage-Dependent Regulators of Germline Stem Cell Division
Smulders-Srinivasan TK, Lin H. Screens for piwi Suppressors in Drosophila Identify Dosage-Dependent Regulators of Germline Stem Cell Division. Genetics 2003, 165: 1971-1991. PMID: 14704180, PMCID: PMC1462913, DOI: 10.1093/genetics/165.4.1971.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, Genetically ModifiedArgonaute ProteinsCell DivisionChromosomesDrosophilaDrosophila ProteinsFemaleGene DosageGene Expression Regulation, DevelopmentalGenes, LethalGerm CellsInfertility, MaleMaleProteinsRNA-Induced Silencing ComplexStem CellsSuppression, GeneticTranscription, GeneticZygoteConceptsStem cell divisionGermline stem cell divisionGenes/sequencesCell divisionFemale-specific lethalityDosage-dependent regulatorGermline stem cellsStem cell maintenanceDrosophila third chromosomeFamily of genesDosage-sensitive mannerPiwi mutantsZygotic functionMutant backgroundPiwi genesThird chromosomeMale germlineMale sterilitySuppressor mutationsSuch genesCell maintenanceGenetic regulationPlant kingdomTranscription factorsTranscriptional level