2019
Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue
Wilkins O, Johnson K, Houseman E, King J, Marsit C, Christensen B. Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue. Epigenetics 2019, 15: 398-418. PMID: 31842685, PMCID: PMC7153548, DOI: 10.1080/15592294.2019.1695332.Peer-Reviewed Original ResearchConceptsGenome-wide characterizationGenome-wide patternsGenome-wide mapsGene regulatory programsActive chromatinGenomic lociGene regulationTranscriptional inactivityRegulatory regionsGene regionMammalian tissuesRegulatory programsCpG lociDNA treatmentImmune cell functionCell functionLociLactate oxidationNormal breast tissueIndependent data setsPre-invasive breast cancerRecent evidenceHeterochromatinChromatinBisulfite
2016
5-Hydroxymethylcytosine localizes to enhancer elements and is associated with survival in glioblastoma patients
Johnson K, Houseman E, King J, von Herrmann K, Fadul C, Christensen B. 5-Hydroxymethylcytosine localizes to enhancer elements and is associated with survival in glioblastoma patients. Nature Communications 2016, 7: 13177. PMID: 27886174, PMCID: PMC5133638, DOI: 10.1038/ncomms13177.Peer-Reviewed Original ResearchMeSH Keywords5-MethylcytosineAdultAgedAged, 80 and overBrain NeoplasmsDNA MethylationDNA, NeoplasmEnhancer Elements, GeneticFemaleGene Expression Regulation, NeoplasticGene Regulatory NetworksGlioblastomaHumansIsocitrate DehydrogenaseMaleMiddle AgedPrefrontal CortexSurvival AnalysisTranscription FactorsConceptsRNA regulatory processesTissue-specific transcriptionDisease critical genesMethylation array dataGenomic distributionGenomic localizationCell maintenanceOxidative bisulfite (oxBS) treatmentTranscription factorsEnhancer elementsPrefrontal cortex tissueBisulfite treatmentCellular proliferationRegulatory processesTranscriptionArray dataMolecular alterationsCortex tissueEpigenomeGlioblastomaImmune functionGenesDNARegulationAnnotationOxyBS: estimation of 5-methylcytosine and 5-hydroxymethylcytosine from tandem-treated oxidative bisulfite and bisulfite DNA
Houseman E, Johnson K, Christensen B. OxyBS: estimation of 5-methylcytosine and 5-hydroxymethylcytosine from tandem-treated oxidative bisulfite and bisulfite DNA. Bioinformatics 2016, 32: 2505-2507. PMID: 27153596, PMCID: PMC4978924, DOI: 10.1093/bioinformatics/btw158.Peer-Reviewed Original Research