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
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
Developmentally regulated extended domains of DNA hypomethylation encompass highly transcribed genes of the human β-globin locus
Lathrop MJ, Hsu M, Richardson CA, Olivier EN, Qiu C, Bouhassira EE, Fiering S, Lowrey CH. Developmentally regulated extended domains of DNA hypomethylation encompass highly transcribed genes of the human β-globin locus. Experimental Hematology 2009, 37: 807-813.e2. PMID: 19460471, PMCID: PMC3792488, DOI: 10.1016/j.exphem.2009.04.005.Peer-Reviewed Original ResearchMeSH KeywordsBeta-GlobinsCpG IslandsDNA MethylationGene Expression Regulation, DevelopmentalHumansPromoter Regions, GeneticTranscription, GeneticConceptsAdult erythroid cellsCpG island genesHistone modificationsGene expressionDNA hypomethylationErythroid cellsDNA methylationBeta-like globin gene expressionBeta-globin gene regulationIsland genesActive histone marksBeta-globin locusGamma-globin promoterGlobin gene expressionHuman embryonic stem cellsDNA methylation patternsSpecific gene expressionEmbryonic stem cellsPrimary human erythroblastsHuman β-globinHistone marksGene regulationMethylation stateBisulfite sequencingCpG islands