Featured Publications
Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation
Roden C, Gaillard J, Kanoria S, Rennie W, Barish S, Cheng J, Pan W, Liu J, Cotsapas C, Ding Y, Lu J. Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation. Genome Research 2017, 27: 374-384. PMID: 28087842, PMCID: PMC5340965, DOI: 10.1101/gr.208900.116.Peer-Reviewed Original ResearchConceptsPri-miRNA processingHuman genetic variationGenetic variationPrimary sequence motifsPrimary microRNA processingMiRNA biogenesisDisease-causing mutationsPrimary miRNAsPri-miRNAsSequence motifsMiRNA hairpinsMicroRNA processingMature microRNAsSequence featuresRNA hairpinsComputational pipelineNovel determinantStem lengthUnpaired basesHairpinTranscriptsStemBiogenesisGenomeMiRNAs
2016
STarMir Tools for Prediction of microRNA Binding Sites
Kanoria S, Rennie W, Liu C, Carmack CS, Lu J, Ding Y. STarMir Tools for Prediction of microRNA Binding Sites. Methods In Molecular Biology 2016, 1490: 73-82. PMID: 27665594, PMCID: PMC5353976, DOI: 10.1007/978-1-4939-6433-8_6.Peer-Reviewed Original ResearchConceptsMessenger RNAEndogenous short noncoding RNAsGene expressionMammalian biological processesHigh-throughput miRNATarget messenger RNAsShort noncoding RNAsMicroRNA Binding SitesCertain human diseasesCross-species validationTranslational repressionMiRNA functionGene regulationSeedless sitesMRNA degradationNoncoding RNAsRegulatory moleculesBiological processesSequence featuresHuman diseasesImmunoprecipitation studiesMiRNAComputational predictionsBinding sitesMiRNAsIn vivo mutagenesis of miRNA gene families using a scalable multiplexed CRISPR/Cas9 nuclease system
Narayanan A, Hill-Teran G, Moro A, Ristori E, Kasper DM, A. Roden C, Lu J, Nicoli S. In vivo mutagenesis of miRNA gene families using a scalable multiplexed CRISPR/Cas9 nuclease system. Scientific Reports 2016, 6: 32386. PMID: 27572667, PMCID: PMC5004112, DOI: 10.1038/srep32386.Peer-Reviewed Original ResearchConceptsMiRNA familiesSingle guide RNAsMiRNA gene familiesHigher multicellular organismsMultiplexed CRISPR/Entire miRNA familiesMulticellular organismsMiRNA genesGene familySame physiological functionChromosomal locationPhylogenetic ancestorsGenomic sequencesCas9 nucleaseGuide RNACRISPR/Mutagenesis strategyNuclease systemPrimary sequenceVivo mutagenesisPhysiological functionsSecondary structureModel systemMiRNAsMutationsIncreased miR-155-5p and reduced miR-148a-3p contribute to the suppression of osteosarcoma cell death
Bhattacharya S, Chalk AM, Ng AJ, Martin TJ, Zannettino AC, Purton LE, Lu J, Baker EK, Walkley CR. Increased miR-155-5p and reduced miR-148a-3p contribute to the suppression of osteosarcoma cell death. Oncogene 2016, 35: 5282-5294. PMID: 27041566, DOI: 10.1038/onc.2016.68.Peer-Reviewed Original ResearchConceptsMiR-148aCell deathCell biological impactMiR-155-5p inhibitionCross-species comparisonsMiR-155-5pApoptosis/necroptosisNormal osteoblastsOS cellsOsteosarcoma cell deathMurine primary osteoblastsMiRNA expression patternsMiRNA-based therapiesCell fateMiR-155-5p overexpressionExpression patternsMolecular geneticsTractable targetsPrimary osteoblastsCandidate targetsBiological impactOsteoblast culturesRIPK1MiRNAsMiRNA
2015
microRNA 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
A 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
An Extensive Network of TET2-Targeting MicroRNAs Regulates Malignant Hematopoiesis
Cheng J, Guo S, Chen S, Mastriano SJ, Liu C, D’Alessio A, Hysolli E, Guo Y, Yao H, Megyola CM, Li D, Liu J, Pan W, Roden CA, Zhou XL, Heydari K, Chen J, Park IH, Ding Y, Zhang Y, Lu J. An Extensive Network of TET2-Targeting MicroRNAs Regulates Malignant Hematopoiesis. Cell Reports 2013, 5: 471-481. PMID: 24120864, PMCID: PMC3834864, DOI: 10.1016/j.celrep.2013.08.050.Peer-Reviewed Original ResearchConceptsKey tumor suppressorMyeloid differentiation biasTET2 expressionTranslocation 2 (TET2) geneMolecular regulationDifferentiation biasHematopoietic malignanciesTen-ElevenMalignant hematopoiesisTumor suppressorHematopoietic expansionActivity screenMiR-7MiRNAsExpression of TET2Normal hematopoiesisOncogenic potentialTET2Important pathogenic mechanismMiR-101Extensive roleMiR-29cHematopoiesisExpressionRegulation
2010
Lineage-Specific Transcriptional Regulation of DICER by MITF in Melanocytes
Levy C, Khaled M, Robinson KC, Veguilla RA, Chen PH, Yokoyama S, Makino E, Lu J, Larue L, Beermann F, Chin L, Bosenberg M, Song JS, Fisher DE. Lineage-Specific Transcriptional Regulation of DICER by MITF in Melanocytes. Cell 2010, 141: 994-1005. PMID: 20550935, PMCID: PMC2897150, DOI: 10.1016/j.cell.2010.05.004.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsApoptosis Regulatory ProteinsBcl-2-Like Protein 11Cell DifferentiationCell SurvivalCells, CulturedEpidermal CellsGene Expression RegulationGene Knockdown TechniquesHair FollicleHumansMelanocytesMembrane ProteinsMiceMice, Inbred C57BLMicrophthalmia-Associated Transcription FactorMicroRNAsPromoter Regions, GeneticProto-Oncogene ProteinsRibonuclease IIITranscription, GeneticUp-RegulationConceptsTranscriptional start siteLineage-specific transcriptional regulationDicer-dependent processingRegulatory element upstreamMITF bindsTranscriptional regulationMature miRNAsProapoptotic regulatorsMiRNA regulationStart siteMelanocyte survivalCentral regulatorDicerMelanocyte differentiationElement upstreamMiRNA expressionCell typesDicer expressionMiRNAsTranscriptional targetingMITFRegulatorMelanocytesExpressionRegulationAberrant overexpression and function of the miR-17-92 cluster in MLL-rearranged acute leukemia
Mi S, Li Z, Chen P, He C, Cao D, Elkahloun A, Lu J, Pelloso LA, Wunderlich M, Huang H, Luo RT, Sun M, He M, Neilly MB, Zeleznik-Le NJ, Thirman MJ, Mulloy JC, Liu PP, Rowley JD, Chen J. Aberrant overexpression and function of the miR-17-92 cluster in MLL-rearranged acute leukemia. Proceedings Of The National Academy Of Sciences Of The United States Of America 2010, 107: 3710-3715. PMID: 20133587, PMCID: PMC2840429, DOI: 10.1073/pnas.0914900107.Peer-Reviewed Original ResearchConceptsMouse bone marrow progenitor cellsMiRNA clusterTarget genesMLL fusionsBone marrow progenitor cellsMiR-17Marrow progenitor cellsCell differentiationDNA copy number amplificationsWild-type MLLProgenitor cellsRelevant target genesHistone H3 acetylationPotential target genesMLL fusion genesCopy number amplificationDevelopment of MLLH3K4 trimethylationIndividual miRNAsH3 acetylationMixed lineage leukemiaCell cycleHuman cellsDirect bindingMiRNAs
2009
microRNA Expression during Trophectoderm Specification
Viswanathan SR, Mermel CH, Lu J, Lu CW, Golub TR, Daley GQ. microRNA Expression during Trophectoderm Specification. PLOS ONE 2009, 4: e6143. PMID: 19582159, PMCID: PMC2702083, DOI: 10.1371/journal.pone.0006143.Peer-Reviewed Original ResearchConceptsEmbryonic stem cellsTrophectoderm specificationPreimplantation developmentMurine embryosFirst cell fate decisionCell fate decisionsTight developmental regulationStem cellsInner cell massCandidate miRNAsNumber of miRNAsStages of embryogenesisRole of microRNAsMiRNA expression changesMammalian developmentTranscription factorsDevelopmental regulationEctopic expressionTarget genesExpression changesTrophectodermal cellsTrophectodermMiRNA expressionFunctional roleMiRNAs
2008
Human multipotent stromal cells from bone marrow and microRNA: Regulation of differentiation and leukemia inhibitory factor expression
Oskowitz AZ, Lu J, Penfornis P, Ylostalo J, McBride J, Flemington EK, Prockop DJ, Pochampally R. Human multipotent stromal cells from bone marrow and microRNA: Regulation of differentiation and leukemia inhibitory factor expression. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 18372-18377. PMID: 19011087, PMCID: PMC2587615, DOI: 10.1073/pnas.0809807105.Peer-Reviewed Original ResearchConceptsHuman multipotent stromal cellsMultipotent stromal cellsAdipogenic differentiationRegulation of differentiationExpression of DicerStromal cellsExpression analysisHMSC differentiationEarly transcriptsFactor expressionMiRNAsLeukemia inhibitory factor expressionOsteogenic differentiationDifferentiationBone marrowExpressionDicerDroshaCellsSilico modelsMicroRNAsMiRNATranscriptsShRNAsEnzymeMicroRNA-Mediated Control of Cell Fate in Megakaryocyte-Erythrocyte Progenitors
Lu J, Guo S, Ebert BL, Zhang H, Peng X, Bosco J, Pretz J, Schlanger R, Wang JY, Mak RH, Dombkowski DM, Preffer FI, Scadden DT, Golub TR. MicroRNA-Mediated Control of Cell Fate in Megakaryocyte-Erythrocyte Progenitors. Developmental Cell 2008, 14: 843-853. PMID: 18539114, PMCID: PMC2688789, DOI: 10.1016/j.devcel.2008.03.012.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntigens, CD34Bone Marrow CellsCell DifferentiationCell LineageCells, CulturedErythroid CellsErythropoietinGene Expression RegulationGenes, ReporterHematopoietic Stem CellsHumansIntegrin beta3K562 CellsMegakaryocytesMiceMice, Inbred C57BLMicroRNAsModels, BiologicalPlatelet Membrane Glycoprotein IIbProto-Oncogene Proteins c-mybThrombopoietinConceptsMegakaryocyte-erythrocyte progenitorsLineage specificationTranscription factor MYBMiR-150Cell fateLineage fateRegenerative biologyErythroid cellsFunction experimentsMultipotent cellsMegakaryocytic lineageMiRNA expressionPrimary cellsCritical targetModel systemMicroRNAsProgenitorsFateRegulationCellsImportant participantsMYBLineagesMiRNAsBiologyDicer-dependent pathways regulate chondrocyte proliferation and differentiation
Kobayashi T, Lu J, Cobb BS, Rodda SJ, McMahon AP, Schipani E, Merkenschlager M, Kronenberg HM. Dicer-dependent pathways regulate chondrocyte proliferation and differentiation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 1949-1954. PMID: 18238902, PMCID: PMC2538863, DOI: 10.1073/pnas.0707900105.Peer-Reviewed Original ResearchConceptsDicer-dependent pathwaysSkeletal developmentBiogenesis of miRNAsMiRNA target genesMammalian skeletal developmentSmall noncoding RNAsSkeletal growth defectsChondrocyte proliferationSuppress gene expressionNormal skeletal developmentDiverse organismsCritical roleGrowth defectNoncoding RNAsRNA abundanceGene expressionExpression changesMicroarray analysisBiological processesSignaling systemMiRNAsBase pairingDistinct mechanismsIhh-PTHrPHypertrophic chondrocytes