2020
Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains
Kentepozidou E, Aitken S, Feig C, Stefflova K, Ibarra-Soria X, Odom D, Roller M, Flicek P. Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains. Genome Biology 2020, 21: 5. PMID: 31910870, PMCID: PMC6945661, DOI: 10.1186/s13059-019-1894-x.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCCCTC-Binding FactorChromatinChromatin Immunoprecipitation SequencingEvolution, MolecularGenomeMiceConceptsTopologically associating domains boundariesTopologically associating domainsCTCF sitesCTCF bindingConservation of topologically associating domainsGenome-wide binding profilesHigher-order chromatin structureCTCF binding patternsCTCF ChIP-seqGene transcription start siteHigher-order genome structureCTCF binding sitesNatural genetic variationTranscription start siteSpecies-specific sitesCohesin stabilizationTAD boundariesChIP-seqGenomic structureStart siteChromatin structureTranscriptional regulationCTCFAssociation domainGenetic variation
2018
CTCF maintains regulatory homeostasis of cancer pathways
Aitken S, Ibarra-Soria X, Kentepozidou E, Flicek P, Feig C, Marioni J, Odom D. CTCF maintains regulatory homeostasis of cancer pathways. Genome Biology 2018, 19: 106. PMID: 30086769, PMCID: PMC6081938, DOI: 10.1186/s13059-018-1484-3.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBreast NeoplasmsCCCTC-Binding FactorCell LineChromatinDNA, NeoplasmEnhancer Elements, GeneticFemaleFibroblastsGene Expression Regulation, NeoplasticGenomeHemizygoteHomeostasisHumansLiver Neoplasms, ExperimentalMiceMice, Inbred C57BLMice, TransgenicProtein BindingSignal TransductionUterine NeoplasmsConceptsTranscriptional regulationIntra-TAD interactionsSteady-state gene expressionCancer-related pathwaysMammalian genomesCTCF occupancyGenome functionChromatin loopsEvolutionary conservationChromatin structureGenomic dysregulationRegulatory domainHemizygous cellsEpigenomic profilingCTCFCTCF expressionMammalian cellsExpressed genesAffinity binding eventsTranscriptional alterationsGene expressionMouse lineagesCancer pathwaysMouse model systemHuman cancers
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