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 basesHairpinTranscriptsStemBiogenesisGenomeMiRNAsA Molecular Chipper technology for CRISPR sgRNA library generation and functional mapping of noncoding regions
Cheng J, Roden CA, Pan W, Zhu S, Baccei A, Pan X, Jiang T, Kluger Y, Weissman SM, Guo S, Flavell RA, Ding Y, Lu J. A Molecular Chipper technology for CRISPR sgRNA library generation and functional mapping of noncoding regions. Nature Communications 2016, 7: 11178. PMID: 27025950, PMCID: PMC4820989, DOI: 10.1038/ncomms11178.Peer-Reviewed Original ResearchAnimalsBacterial ProteinsCell LineChromosome MappingCloning, MolecularClustered Regularly Interspaced Short Palindromic RepeatsCRISPR-Associated Protein 9DNADNA Restriction EnzymesEndonucleasesGene LibraryGenomeHumansMiceMicroRNAsOligonucleotide Array Sequence AnalysisRNA, Guide, CRISPR-Cas SystemsUntranslated Regions
2015
Characterization of the mammalian miRNA turnover landscape
Guo Y, Liu J, Elfenbein SJ, Ma Y, Zhong M, Qiu C, Ding Y, Lu J. Characterization of the mammalian miRNA turnover landscape. Nucleic Acids Research 2015, 43: 2326-2341. PMID: 25653157, PMCID: PMC4344502, DOI: 10.1093/nar/gkv057.Peer-Reviewed Original ResearchConceptsMiRNA turnoverStable small RNAsMammalian cell typesCultured mammalian cellsSubset of miRNAsTurnover kineticsMiRNA biogenesisMost miRNAsMiR-222-5pNucleotide biasSmall RNAsMiRNA maturationMammalian cellsSame miRNAMiRNA poolExpression profilingHsp90 associationSequence determinantsDeep sequencingHsp90 inhibitionTurnover rateMiRNA isoformsDifferent turnover ratesSequence featuresCell types
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
2012
miR-1 and miR-206 regulate angiogenesis by modulating VegfA expression in zebrafish
Stahlhut C, Suárez Y, Lu J, Mishima Y, Giraldez AJ. miR-1 and miR-206 regulate angiogenesis by modulating VegfA expression in zebrafish. Development 2012, 139: 4356-4365. PMID: 23132244, PMCID: PMC3509730, DOI: 10.1242/dev.083774.Peer-Reviewed Original ResearchConceptsMiR-1/206Post-transcriptional modulatorsMiRNA-target interactionsMiR-1Appropriate physiological responsesRegulation of VEGFAZebrafish developmentEmbryonic developmentTarget protectorNovel functionPrecise regulationGene expressionMorphogenetic activityDevelopmental angiogenesisPutative targetsRegulate angiogenesisEssential processMiR-206Physiological responsesCellular communicationVEGFA expressionGrowth factorVascular endothelial growth factorExpressionAngiogenesisComplex oncogene dependence in microRNA-125a–induced myeloproliferative neoplasms
Guo S, Bai H, Megyola CM, Halene S, Krause DS, Scadden DT, Lu J. Complex oncogene dependence in microRNA-125a–induced myeloproliferative neoplasms. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 16636-16641. PMID: 23012470, PMCID: PMC3478612, DOI: 10.1073/pnas.1213196109.Peer-Reviewed Original ResearchAnimalsBone Marrow CellsBone Marrow NeoplasmsBone Marrow TransplantationCell LineColony-Forming Units AssayDoxycyclineFlow CytometryGene Expression Regulation, NeoplasticGranulocyte-Macrophage Colony-Stimulating FactorInterleukin-3Leukocytes, MononuclearMiceMice, Inbred C57BLMicroRNAsMyeloproliferative DisordersOncogenesReverse Transcriptase Polymerase Chain Reaction
2008
The Growth Factor Environment Defines Distinct Pluripotent Ground States in Novel Blastocyst-Derived Stem Cells
Chou YF, Chen HH, Eijpe M, Yabuuchi A, Chenoweth JG, Tesar P, Lu J, McKay RD, Geijsen N. The Growth Factor Environment Defines Distinct Pluripotent Ground States in Novel Blastocyst-Derived Stem Cells. Cell 2008, 135: 449-461. PMID: 18984157, PMCID: PMC2767270, DOI: 10.1016/j.cell.2008.08.035.Peer-Reviewed Original ResearchConceptsStem cell linesGrowth factor environmentPluripotent stateTissue of originCell linesEmbryonic stem cell linesPluripotent ground stateBlastocyst embryosStem cell identityCell-cell interactionsGrowth factor conditionsStem cell typesFactor environmentPostimplantation epiblastCell identityES cellsDevelopmental stagesCell typesStem cellsFunctional differencesCritical roleEmbryosGrowth factorGrowth factor milieuEpiSCs
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 region