2012
A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells
Charos AE, Reed BD, Raha D, Szekely AM, Weissman SM, Snyder M. A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells. Genome Research 2012, 22: 1668-1679. PMID: 22955979, PMCID: PMC3431484, DOI: 10.1101/gr.127761.111.Peer-Reviewed Original ResearchMeSH KeywordsBinding SitesCarrier ProteinsChromatin ImmunoprecipitationCluster AnalysisGene Expression RegulationGene Regulatory NetworksHeat-Shock ProteinsHep G2 CellsHigh-Throughput Nucleotide SequencingHumansNucleotide MotifsPeroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alphaProtein BindingProtein TransportTranscription FactorsTranscription, GeneticConceptsTranscription factorsGenome-wide binding sitesCombinatorial binding patternsHeat shock response pathwayIndividual transcription factorsTranscriptional regulatory networksDNA sequence motifsDifferent transcription factorsShock response pathwayHigh-throughput sequencingMetabolic gene expressionHepG2 cellsTF partnersTranscriptional dynamicsCellular processesChIP-seqSequence motifsRegulatory networksTranscriptional coactivatorResponse pathwaysInterdependent regulationTarget genesChromatin IPRegulatory codeGene expression
2008
Genome-Wide Occupancy of SREBP1 and Its Partners NFY and SP1 Reveals Novel Functional Roles and Combinatorial Regulation of Distinct Classes of Genes
Reed BD, Charos AE, Szekely AM, Weissman SM, Snyder M. Genome-Wide Occupancy of SREBP1 and Its Partners NFY and SP1 Reveals Novel Functional Roles and Combinatorial Regulation of Distinct Classes of Genes. PLOS Genetics 2008, 4: e1000133. PMID: 18654640, PMCID: PMC2478640, DOI: 10.1371/journal.pgen.1000133.Peer-Reviewed Original ResearchConceptsTarget genesGenome-wide occupancyDNA-binding motifComplex transcriptional responseGenome tiling arraysDiverse biological pathwaysSREBP1 target genesCritical transcriptional regulatorNovel functional roleGene expression microarraysDistinct functional pathwaysCombinatorial regulationTarget promotersTranscriptional regulatorsTiling arraysRegulatory circuitryTranscriptional responseChromatin immunoprecipitationFatty acid metabolismExpression microarraysFunctional pathwaysBiological pathwaysHepatocyte cell lineHuman hepatocyte cell lineSp1
2005
Werner Protein Protects Nonproliferating Cells from Oxidative DNA Damage
Szekely AM, Bleichert F, Nümann A, Van Komen S, Manasanch E, Nasr A, Canaan A, Weissman SM. Werner Protein Protects Nonproliferating Cells from Oxidative DNA Damage. Molecular And Cellular Biology 2005, 25: 10492-10506. PMID: 16287861, PMCID: PMC1291253, DOI: 10.1128/mcb.25.23.10492-10506.2005.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesCell ProliferationCells, CulturedCellular SenescenceDNADNA DamageDNA HelicasesDNA ReplicationExodeoxyribonucleasesFibroblastsGene Expression RegulationHumansOxidation-ReductionOxidative StressOxygenRecQ HelicasesRNA InterferenceTelomeric Repeat Binding Protein 2Werner Syndrome HelicaseConceptsDNA damage responseWerner syndromeDamage responseDNA damageRNA interferenceOxidative DNA damageWRN-depleted cellsInduction of gammaH2AXDNA damage fociCellular senescence phenotypePrimary human fibroblastsWRN depletionWerner proteinWRN proteinNuclear fociWRN deficiencyProtein TRF2Telomere maintenanceAcute oxidative stressBLM expressionDNA homeostasisDNA replicationDamage fociSenescence phenotypePhysiological oxygen