2019
Sfold Tools for MicroRNA Target Prediction
Rennie W, Kanoria S, Liu C, Carmack CS, Lu J, Ding Y. Sfold Tools for MicroRNA Target Prediction. Methods In Molecular Biology 2019, 1970: 31-42. PMID: 30963486, DOI: 10.1007/978-1-4939-9207-2_3.Peer-Reviewed Original Research
2018
ZEB1, ZEB2, and the miR-200 family form a counterregulatory network to regulate CD8+ T cell fates
Guan T, Dominguez CX, Amezquita RA, Laidlaw BJ, Cheng J, Henao-Mejia J, Williams A, Flavell RA, Lu J, Kaech SM. ZEB1, ZEB2, and the miR-200 family form a counterregulatory network to regulate CD8+ T cell fates. Journal Of Experimental Medicine 2018, 215: 1153-1168. PMID: 29449309, PMCID: PMC5881466, DOI: 10.1084/jem.20171352.Peer-Reviewed Original ResearchConceptsT cellsMemory CD8T cell fateMemory T cell survivalLong-term immunityT cell formationT cell survivalMiR-200 family membersGrowth factor βFamily membersTranscription factor ZEB1Effector CD8MiR-200 familyCD8Mesenchymal transitionReciprocal expression patternCell fateZEB1ZEB2Factor βCell survivalTGFCell formationUnknown genetic pathwaysCell fate decisions
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 sitesMiRNAs
2014
Effects of genetic variations on microRNA: target interactions
Liu C, Rennie WA, Carmack CS, Kanoria S, Cheng J, Lu J, Ding Y. Effects of genetic variations on microRNA: target interactions. Nucleic Acids Research 2014, 42: 9543-9552. PMID: 25081214, PMCID: PMC4150780, DOI: 10.1093/nar/gku675.Peer-Reviewed Original ResearchMeSH KeywordsBinding SitesDiseaseGenetic VariationHumansMicroRNAsPhenotypePolymorphism, Single NucleotideRNA, MessengerConceptsMiRNA binding sitesGenetic variationGene regulationGenetic variantsMiRNA-mediated gene regulationBinding sitesModulation of miRNAPotential of miRNARare variantsLow mutation frequencyFlanking regionsHuman diseasesVariant densityStructural accessibilityMiRNACommon variantsMutation frequencyMicroRNAsTarget interactionsRegulationStructure alterationsVariantsNew associationsTranscriptomeSitesSTarMir: a web server for prediction of microRNA binding sites
Rennie W, Liu C, Carmack CS, Wolenc A, Kanoria S, Lu J, Long D, Ding Y. STarMir: a web server for prediction of microRNA binding sites. Nucleic Acids Research 2014, 42: w114-w118. PMID: 24803672, PMCID: PMC4086099, DOI: 10.1093/nar/gku376.Peer-Reviewed Original Research
2013
The IGF2 intronic miR-483 selectively enhances transcription from IGF2 fetal promoters and enhances tumorigenesis
Liu M, Roth A, Yu M, Morris R, Bersani F, Rivera MN, Lu J, Shioda T, Vasudevan S, Ramaswamy S, Maheswaran S, Diederichs S, Haber DA. The IGF2 intronic miR-483 selectively enhances transcription from IGF2 fetal promoters and enhances tumorigenesis. Genes & Development 2013, 27: 2543-2548. PMID: 24298054, PMCID: PMC3861668, DOI: 10.1101/gad.224170.113.Peer-Reviewed Original ResearchConceptsInsulin-like growth factor 2Loss of imprintingUntranslated regionFunctional positive feedback loopRNA helicase DHX9IGF2 mRNAAdditional regulatory mechanismsIntronic miRNANuclear poolHost genesEctopic expressionMicroRNA screenPositive feedback loopIGF2 transcriptionPrimary Wilms tumorsFetal promotersIGF2 transcriptsPromoter contributesRegulatory mechanismsIGF2 geneGrowth factor 2IGF2 expressionTranscriptionGenesMiR-483
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 modelsMicroRNAsMiRNATranscriptsShRNAsEnzyme
2006
Microarray-Assisted Pathway Analysis Identifies Mitogen-Activated Protein Kinase Signaling as a Mediator of Resistance to the Green Tea Polyphenol Epigallocatechin 3-Gallate in Her-2/neu–Overexpressing Breast Cancer Cells
Guo S, Lu J, Subramanian A, Sonenshein GE. Microarray-Assisted Pathway Analysis Identifies Mitogen-Activated Protein Kinase Signaling as a Mediator of Resistance to the Green Tea Polyphenol Epigallocatechin 3-Gallate in Her-2/neu–Overexpressing Breast Cancer Cells. Cancer Research 2006, 66: 5322-5329. PMID: 16707458, DOI: 10.1158/0008-5472.can-05-4287.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnticarcinogenic AgentsCatechinCell AdhesionCell Growth ProcessesDexamethasoneDrug Resistance, NeoplasmEnzyme ActivationMammary Neoplasms, ExperimentalMAP Kinase Signaling SystemMiceMitogen-Activated Protein KinasesNF-kappa BOligonucleotide Array Sequence AnalysisPhosphorylationReceptor, ErbB-2RNA, Messenger
2002
A selective effect of Mpl ligand on mRNA stabilization during megakaryocyte differentiation
Kaluzhny Y, Hechler B, Lu J, Nguyen HG, Cataldo LM, Ravid K. A selective effect of Mpl ligand on mRNA stabilization during megakaryocyte differentiation. FEBS Letters 2002, 527: 279-283. PMID: 12220674, DOI: 10.1016/s0014-5793(02)03230-1.Peer-Reviewed Original Research3' Flanking Region3' Untranslated RegionsAnimalsCell DifferentiationCells, CulturedGlyceraldehyde-3-Phosphate DehydrogenasesMegakaryocytesMiceNeoplasm ProteinsPlatelet Factor 4Promoter Regions, GeneticProto-Oncogene ProteinsReceptors, CytokineReceptors, Purinergic P2Receptors, Purinergic P2Y1Receptors, ThrombopoietinRNA StabilityRNA, MessengerThrombopoietin
1999
Mpl ligand enhances the transcription of the cyclin D3 gene: a potential role for Sp1 transcription factor.
Wang Z, Zhang Y, Lu J, Sun S, Ravid K. Mpl ligand enhances the transcription of the cyclin D3 gene: a potential role for Sp1 transcription factor. Blood 1999, 93: 4208-21. PMID: 10361118, DOI: 10.1182/blood.v93.12.4208.412k17_4208_4221.Peer-Reviewed Original ResearchConceptsProtein phosphatase 1Cyclin D3 promoterMpl ligandCyclin D3 geneTranscription factorsSp1-dependent genesD3 geneSp1 transcription factorForm of Sp1Basal promoter activityMegakaryocytic cell linesCyclin D3 proteinSp familySp1 proteinD3 gene expressionSp1 sitesPhosphatase 1Okadaic acidCyclin D3 gene expressionNuclear runSp1DNase IGene expressionPromoter activityPromoter regionRat NAP1: cDNA cloning and upregulation by Mpl ligand
Cataldo L, Zhang Y, Lu J, Ravid K. Rat NAP1: cDNA cloning and upregulation by Mpl ligand. Gene 1999, 226: 355-364. PMID: 9931510, DOI: 10.1016/s0378-1119(98)00563-0.Peer-Reviewed Original ResearchMeSH KeywordsAgingAmino Acid SequenceAnimalsBase SequenceBone Marrow CellsCell Cycle ProteinsCell LineageCells, CulturedCloning, MolecularDNA, ComplementaryGene Expression RegulationMolecular Sequence DataNuclear ProteinsNucleosome Assembly Protein 1ProteinsRatsReverse Transcriptase Polymerase Chain ReactionRNA, MessengerSequence Homology, Amino AcidThrombopoietinUp-RegulationConceptsMpl ligandNucleosome assembly proteinPrimary bone marrow cellsFull-length cDNASize classesFormation of nucleosomesC-Mpl receptorChromatin reorganizationMultiple size classesAssembly proteinPolymerase chain reaction approachRelaxed circular DNACDNA cloningKb cDNAHematopoietic lineagesKb mRNARecombinant proteinsHematopoietic cytokinesHematopoietic cellsCircular DNAPlatelet precursorsBone marrow cellsHematopoietic tissuesCell linesCDNA