Project description:To test the genomic region containing rs2431697 whether forms a cognate enhancer-promoter loop with the miR-146a promoter and modulates the expression of miR-146a, we perfomed 4C-seq in U-937 cell line based on the rs2431697 view point and miR-146a promoter view point.
Project description:The study uncovers epigenomic changes associated with dexamethasone response heterogeneity in myeloma cells, revealing rewired promoter-enhancer interactions and DNA loop stabilization
Project description:To test the genomic region containing rs2431697 whether forms a cognate enhancer-promoter loop with the miR-146a promoter and modulates the expression of miR-146a, we perfomed 4C-seq in U-937 cell line based on miR-146a promoter view point (First digestion enzyme MboI, second digestion enzyme NlaIII) and rs2431697 view point (First digestion enzyme CSP6I, second digestion enzyme NlaIII).
Project description:Enhancers harbor instructions encoded for the interactions between cis-elements and transcription factors to orchestrate lineage specific gene programs. Here we developed a modified method for chromosome conformation capture (3C), named MID Hi-C, to reveal how in mouse embryonic stem cells differential cooperation of enhancers and the chromatin remodeler BAF, as instructed by the underlying transcription factor motifs, modulate enhancer-promoter communication. We show that BAF-dependent enhancers permit genomic interactions beyond enhancer boundaries. BAF-dependent enhancers do not dictate genomic interactions within enhancer-promoter loop domains but rather act to instruct remote enhancer-promoter communication. In contrast, BAF-independent enhancers interact with promoter regions within tightly insulated enhancer-promoter loop domains that are marked by promoter and enhancer boundary elements. In addition, enhancer activeness modulated by BAF enforces compartment segregation. Based on these observations, we propose that enhancer cis elements instruct with great precision BAF-induced enhancer-promoter communication and compartmental segregation.