2021
Genome-wide mapping of Piwi association with specific loci in Drosophila ovaries
Liu N, Neuenkirchen N, Zhong M, Lin H. Genome-wide mapping of Piwi association with specific loci in Drosophila ovaries. G3: Genes, Genomes, Genetics 2021, 11: jkaa059. PMID: 33609367, PMCID: PMC8022938, DOI: 10.1093/g3journal/jkaa059.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsProtein-coding genesDrosophila ovaryGermline stem cell maintenanceRole of piRNAsTermination sitesGenome-wide mappingGenomic binding profileTranscriptional termination sitesSpecific genomic sitesStem cell maintenanceRNA pathwaysTransposon repressionTranscriptional startEuchromatic regionsGene regulationEpigenetic regulationGenomic sitesCell maintenancePiwiSpecific lociMethylation signalsDiverse mechanismsTarget siteBinding sites
2018
An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
Terranova C, Tang M, Orouji E, Maitituoheti M, Raman A, Amin S, Liu Z, Rai K. An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues. Journal Of Visualized Experiments 2018 DOI: 10.3791/56972-v.Peer-Reviewed Original Research
2017
Comparative analysis reveals genomic features of stress-induced transcriptional readthrough
Vilborg A, Sabath N, Wiesel Y, Nathans J, Levy-Adam F, Yario TA, Steitz JA, Shalgi R. Comparative analysis reveals genomic features of stress-induced transcriptional readthrough. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: e8362-e8371. PMID: 28928151, PMCID: PMC5635911, DOI: 10.1073/pnas.1711120114.Peer-Reviewed Original ResearchConceptsTranscriptional readthroughReadthrough transcriptionGenomic featuresOsmotic stressProtein-coding gene lociHeat shockUnique chromatin signatureGenome-wide mappingOpen chromatin statePolymerase II occupancyNuclear RNA-seqGenome-wide studiesChromatin signaturesChromatin stateNIH 3T3 mouse fibroblast cellsNeighboring genesRNA classesReadthrough transcriptsReadthrough phenomenonRegulated processRNA-seqGene transcriptionGene locusStress responsePotential regulatorDynamic regulation of Nanog and stem cell-signaling pathways by Hoxa1 during early neuro-ectodermal differentiation of ES cells
De Kumar B, Parker H, Parrish M, Lange J, Slaughter B, Unruh J, Paulson A, Krumlauf R. Dynamic regulation of Nanog and stem cell-signaling pathways by Hoxa1 during early neuro-ectodermal differentiation of ES cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: 5838-5845. PMID: 28584089, PMCID: PMC5468655, DOI: 10.1073/pnas.1610612114.Peer-Reviewed Original ResearchConceptsES cell differentiationRegulatory networksMutual repressionRegulatory regionsCell differentiationCore pluripotency networkGenome-wide mappingRegulation of pluripotencyPatterns of occupancyCell-signaling pathwaysPluripotency networkNanog bindsHox genesGenomic approachesCommon target sitesRetinoic acid treatmentTarget genesDynamic regulationES cellsMouse embryosMolecular mechanismsHOXA1GenesAlternate statesNanog
2014
Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains
Bai G, Cheung I, Shulha H, Coelho J, Li P, Dong X, Jakovcevski M, Wang Y, Grigorenko A, Jiang Y, Hoss A, Patel K, Zheng M, Rogaev E, Myers R, Weng Z, Akbarian S, Chen J. Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains. Human Molecular Genetics 2014, 24: 1441-1456. PMID: 25480889, PMCID: PMC4321450, DOI: 10.1093/hmg/ddu561.Peer-Reviewed Original ResearchMeSH KeywordsAdultAutopsyBasic Helix-Loop-Helix Transcription FactorsCase-Control StudiesCell Line, TumorChromatin ImmunoprecipitationDNA MethylationEpigenesis, GeneticFemaleGenetic LociGenetic MarkersGenome-Wide Association StudyHigh-Throughput Nucleotide SequencingHomeodomain ProteinsHumansHuntington DiseaseMaleNeostriatumNeuronsPhylogenyPromoter Regions, GeneticRNA, MessengerRNA, Small InterferingTranscription Factor HES-1ConceptsHuntington's diseaseGenome-wide distribution of H3K4me3Reduced binding of nuclear proteinsLoss of H3K4me3Genome-wide distributionEpigenetic dysregulationGenome-wide mappingCpG-rich sequencesDistribution of H3K4me3Binding of nuclear proteinsExcessive DNA methylationNotch signaling genesP21 mRNA expressionHuman neuroblastoma cellsPromoter sequencesNeuronal epigenomeTranscriptional marksChromatin immunoprecipitationMethylation regionsDNA methylationNuclear proteinsDeep sequencingEpigenetic contributionsHD brainSignaling Genes
2013
Large conserved domains of low DNA methylation maintained by Dnmt3a
Jeong M, Sun D, Luo M, Huang Y, Challen G, Rodriguez B, Zhang X, Chavez L, Wang H, Hannah R, Kim S, Yang L, Ko M, Chen R, Göttgens B, Lee J, Gunaratne P, Godley L, Darlington G, Rao A, Li W, Goodell M. Large conserved domains of low DNA methylation maintained by Dnmt3a. Nature Genetics 2013, 46: 17-23. PMID: 24270360, PMCID: PMC3920905, DOI: 10.1038/ng.2836.Peer-Reviewed Original ResearchMeSH Keywords5-MethylcytosineAnimalsBase SequenceConserved SequenceCpG IslandsCytosineDatabases, GeneticDNA (Cytosine-5-)-MethyltransferasesDNA MethylationDNA Methyltransferase 3AEpigenesis, GeneticGene Expression RegulationHematopoietic Stem CellsHistonesHumansLeukemiaMaleMiceMice, Inbred C57BLMice, Mutant Strains
2012
DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells
Alexandrov BS, Fukuyo Y, Lange M, Horikoshi N, Gelev V, Rasmussen KØ, Bishop AR, Usheva A. DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells. Nucleic Acids Research 2012, 40: 10116-10123. PMID: 22904068, PMCID: PMC3488223, DOI: 10.1093/nar/gks758.Peer-Reviewed Original ResearchConceptsTranscription factorsGenome-wide mappingProtein-DNA bindingGene expression regulatorsEssential biological processesTranscription factor YY1DNA binding sitesDNA breathing dynamicsGenomic functionsYY1 bindingFactor YY1Expression regulatorsPhenotypic diversityConsensus sitesSequence variationGel shiftBiological processesCellular behaviorSequence contextFunctional SNPsYY1Strand separationBreathing dynamicsDNA dynamicsBinding sitesModeling gene expression using chromatin features in various cellular contexts
Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z. Modeling gene expression using chromatin features in various cellular contexts. Genome Biology 2012, 13: r53. PMID: 22950368, PMCID: PMC3491397, DOI: 10.1186/gb-2012-13-9-r53.Peer-Reviewed Original ResearchConceptsChromatin featuresRNA-seqExpression levelsGene expressionPolyA RNADNase I hypersensitivity sitesGenome-wide mappingCell linesDifferent cellular contextsDifferent cellular compartmentsDifferent cell compartmentsGene expression levelsHigh-throughput techniquesHistone variantsHistone marksTranscriptional regulationHuman cell linesRNA-PETENCODE projectCellular contextCellular compartmentsCytosolic RNANuclear RNAHypersensitivity sitesRNA
2011
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nature Protocols 2011, 6: 468-481. PMID: 21412275, DOI: 10.1038/nprot.2010.190.Peer-Reviewed Original ResearchConceptsSingle-nucleotide resolutionGenome-scale DNA methylation profilingCpG-rich DNA fragmentsGenome-wide mappingGenome-wide scaleStandard molecular biology laboratoryMajority of promotersRelevant genomic regionsIllumina Genome AnalyzerNext-generation sequencing approachDNA methylation profilingDNA methylation measurementsRestriction enzyme MspIReduced representationMolecular biology laboratoryGenomic regionsRRBS librariesGenome AnalyzerSequencing librariesMethylation profilingSequencing approachEnzyme MspIAmount of sequencingLow input requirementsGenomic DNA
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