2010
Genome-wide methylation and expression profiling identifies promoter characteristics affecting demethylation-induced gene up-regulation in melanoma
Rubinstein JC, Tran N, Ma S, Halaban R, Krauthammer M. Genome-wide methylation and expression profiling identifies promoter characteristics affecting demethylation-induced gene up-regulation in melanoma. BMC Medical Genomics 2010, 3: 4. PMID: 20144234, PMCID: PMC2843643, DOI: 10.1186/1755-8794-3-4.Peer-Reviewed Original ResearchMeSH KeywordsAgedAntimetabolites, AntineoplasticAzacitidineCell Line, TumorCpG IslandsDecitabineDNA MethylationDNA Modification MethylasesEnzyme InhibitorsEpigenesis, GeneticFemaleGene Expression ProfilingGenome, HumanHumansMaleMelanomaMiddle AgedPromoter Regions, GeneticTumor Suppressor ProteinsUp-RegulationConceptsHigh CpG contentCpG contentGenome-wide gene expression dataMethylation levelsPromoter CpG contentUp-regulates gene expressionGenome-wide methylationGenome-wide dataLow CpG contentMelanoma cell strainsGene expression dataTumor suppressor geneCytosine analog 5Lower methylation levelsTranscriptional silencingMethylated promotersHigher methylation levelsBisulfite sequencingDNA methylationCpG methylationDNA methyltransferaseGenomic hypomethylationPromoter characteristicsSpecific genesGene expression
2009
Integrative Analysis of Epigenetic Modulation in Melanoma Cell Response to Decitabine: Clinical Implications
Halaban R, Krauthammer M, Pelizzola M, Cheng E, Kovacs D, Sznol M, Ariyan S, Narayan D, Bacchiocchi A, Molinaro A, Kluger Y, Deng M, Tran N, Zhang W, Picardo M, Enghild JJ. Integrative Analysis of Epigenetic Modulation in Melanoma Cell Response to Decitabine: Clinical Implications. PLOS ONE 2009, 4: e4563. PMID: 19234609, PMCID: PMC2642998, DOI: 10.1371/journal.pone.0004563.Peer-Reviewed Original ResearchConceptsDNA damage responseMelanoma cell responseDamage responseGene expressionIntegrative analysisDifferential gene expressionMelanoma cell strainsGene expression profilesDNA promoter methylationP53-independent mannerHistone modificationsImproved combination therapiesEpigenetic modifiersTGFbeta pathwayBioinformatics analysisProtein stabilityEpigenetic modulationResistant melanoma cellsExpression profilesGrowth arrestPromoter methylationCancer cellsCell strainsProteasome inhibitorsPTEN mutations
2008
MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment
Pelizzola M, Koga Y, Urban AE, Krauthammer M, Weissman S, Halaban R, Molinaro AM. MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. Genome Research 2008, 18: 1652-1659. PMID: 18765822, PMCID: PMC2556264, DOI: 10.1101/gr.080721.108.Peer-Reviewed Original ResearchConceptsDNA methylation levelsDNA methylationMethylation levelsRelative DNA methylation levelsChromosome-wide levelBisulfite genomic DNA sequencingGenome-wide studiesMelanoma cell strainsDNA methylation statusGenomic DNA sequencingTranscriptional machineryNormal human melanocytesMethylated CpGsMethylated fragmentsEpigenetic modificationsMethylation estimatesHigh-throughput settingHuman diseasesHuman melanocytesMethylationMethylation statusDNA sequencingAntibody enrichmentGenomeCell strains
2006
Rab33A: Characterization, Expression, and Suppression by Epigenetic Modification
Cheng E, Trombetta SE, Kovacs D, Beech RD, Ariyan S, Reyes-Mugica M, McNiff JM, Narayan D, Kluger HM, Picardo M, Halaban R. Rab33A: Characterization, Expression, and Suppression by Epigenetic Modification. Journal Of Investigative Dermatology 2006, 126: 2257-2271. PMID: 16810302, DOI: 10.1038/sj.jid.5700386.Peer-Reviewed Original ResearchConceptsX chromosome-linked geneSpecific gene expressionTranscription initiation siteSpecific promoter regionsMelanoma cellsGTPase mutantsEpigenetic modificationsSmall GTPaseDNA methylationVesicular transportRab33AGene expressionPromoter regionMelanosomal proteinsInitiation siteNormal melanocytesAberrant downregulationGenesEarly eventsAberrant processesMelanocytesExpressionGTPaseImportant roleNormal process