2023
DNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain-specific PKMζ
Pramio D, Vieceli F, Varella-Branco E, Goes C, Kobayashi G, da Silva Pelegrina D, de Moraes B, El Allam A, De Kumar B, Jara G, Farfel J, Bennett D, Kundu S, Viapiano M, Reis E, de Oliveira P, Dos Santos E Passos-Bueno M, Rothlin C, Ghosh S, Schechtman D. DNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain-specific PKMζ. Biochimica Et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2023, 1866: 194909. PMID: 36682583, PMCID: PMC10037092, DOI: 10.1016/j.bbagrm.2023.194909.Peer-Reviewed Original ResearchMeSH KeywordsAlzheimer DiseaseBrainCyclic AMP Response Element-Binding ProteinDNA MethylationEpigenesis, GeneticHumansLong-Term PotentiationConceptsInduced pluripotent stem cellsInternal promoterNeuronal differentiationEpigenetic mechanismsDNA methylationUpstream promoterProtein kinase C ζHuman neuronal differentiationSite-specific hypermethylationAberrant DNA hypermethylationPluripotent stem cellsEpigenetic regulationSame epigenetic mechanismsLong-term memory formationDNA hypermethylationDemethylated regionsEpigenetic factorsPromoter regionTissue specificityMolecular mechanismsPRKCZ geneDifferentiated neuronsPromoterProtein kinase M zetaLong-term potentiation
2018
Retinoid-Sensitive Epigenetic Regulation of the Hoxb Cluster Maintains Normal Hematopoiesis and Inhibits Leukemogenesis
Qian P, De Kumar B, He X, Nolte C, Gogol M, Ahn Y, Chen S, Li Z, Xu H, Perry J, Hu D, Tao F, Zhao M, Han Y, Hall K, Peak A, Paulson A, Zhao C, Venkatraman A, Box A, Perera A, Haug J, Parmely T, Li H, Krumlauf R, Li L. Retinoid-Sensitive Epigenetic Regulation of the Hoxb Cluster Maintains Normal Hematopoiesis and Inhibits Leukemogenesis. Cell Stem Cell 2018, 22: 740-754.e7. PMID: 29727682, DOI: 10.1016/j.stem.2018.04.012.Peer-Reviewed Original ResearchConceptsHoxb expressionHematopoietic stem cellsDNA methylationCoordinate regulationLoss of HSCsCis-regulatory elementsSpecific DNA methylationDNA methylome analysisHox genesHOXB clusterHox expressionEpigenetic regulationDNA methyltransferasesMethylome analysisHoxb genesCluster expressionLT-HSCsRetinoid signalingNormal hematopoiesisGenesStem cellsLeukemogenesisMethylationReconstitution capacityRegulation
2015
Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells
De Kumar B, Parrish M, Slaughter B, Unruh J, Gogol M, Seidel C, Paulson A, Li H, Gaudenz K, Peak A, McDowell W, Fleharty B, Ahn Y, Lin C, Smith E, Shilatifard A, Krumlauf R. Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells. Genome Research 2015, 25: 1229-1243. PMID: 26025802, PMCID: PMC4510006, DOI: 10.1101/gr.184978.114.Peer-Reviewed Original ResearchConceptsChromatin modificationsHomeotic clustersHox genesES cellsClustered Hox genesHomeotic gene transcriptionMouse embryonic stem cellsNoncoding RNA genesRetinoid-induced transcriptionGenome-wide approachesCis-regulatory elementsEmbryonic stem cellsTranscription stateChromatin marksHOXB clusterNoncoding genesRNA genesSegmental identityActive transcriptionNoncoding RNAsTranscription factorsEpigenetic profilesGene transcriptionEpigenetic changesBody axis