2023
Spatial epigenome–transcriptome co-profiling of mammalian tissues
Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija G, Dwork A, Mann J, Leong K, Boldrini M, Wang L, Haeussler M, Raphael B, Kluger Y, Castelo-Branco G, Fan R. Spatial epigenome–transcriptome co-profiling of mammalian tissues. Nature 2023, 616: 113-122. PMID: 36922587, PMCID: PMC10076218, DOI: 10.1038/s41586-023-05795-1.Peer-Reviewed Original ResearchConceptsGene expressionSingle-cell resolutionChromatin accessibilityJoint profilingHistone modificationsGene regulationCellular statesEpigenetic mechanismsCentral dogmaSpatial transcriptomeTranscriptional phenotypeCell statesOmics informationSpatial transcriptomicsEpigenetic primingMammalian tissuesEpigenomeMolecular biologyTissue architectureCell dynamicsMechanistic relationshipDifferential rolesNew insightsMouse brainProfiling
2016
Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions
Jiang T, Raviram R, Snetkova V, Rocha PP, Proudhon C, Badri S, Bonneau R, Skok JA, Kluger Y. Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions. Nucleic Acids Research 2016, 44: 8714-8725. PMID: 27439714, PMCID: PMC5062970, DOI: 10.1093/nar/gkw568.Peer-Reviewed Original ResearchConceptsMulti-locus interactionsDNA FISHGene regulationChromosome conformation capture techniquesFunctional importancePairwise chromatin interactionsChromatin interactionsTranscriptional outputRegulatory elementsEnhancer elementsBiological settingsSame cellsSimultaneous interactionFishNew insightsEnhancerRegulationReceptor enhancerCapture techniquesInteractionTCRB