2015
Reassessment of Piwi Binding to the Genome and Piwi Impact on RNA Polymerase II Distribution
Lin H, Chen M, Kundaje A, Valouev A, Yin H, Liu N, Neuenkirchen N, Zhong M, Snyder M. Reassessment of Piwi Binding to the Genome and Piwi Impact on RNA Polymerase II Distribution. Developmental Cell 2015, 32: 772-774. PMID: 25805139, PMCID: PMC4472434, DOI: 10.1016/j.devcel.2015.03.004.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArgonaute ProteinsBase SequenceBinding SitesChromatin ImmunoprecipitationChromobox Protein Homolog 5Chromosomal Proteins, Non-HistoneDNA-Binding ProteinsDrosophila melanogasterDrosophila ProteinsGenomeHigh-Throughput Nucleotide SequencingHistone MethyltransferasesHistone-Lysine N-MethyltransferaseMethyltransferasesRNA InterferenceRNA Polymerase IIRNA, Small InterferingSequence Analysis, DNAConceptsRNA polymerase II distributionGenomic targetsHeterochromatin protein 1aRNA polymerase IICurrent bioinformatics methodsPiwi mutantsDrosophila PiwiPolymerase IIDevelopmental cellsPericentric regionsHistone methyltransferaseBioinformatics methodsBioinformatics pipelineProtein 1APiwiGenomePiRNAsEuchromatinMutantsMethyltransferaseSites
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