GSE116721
Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions [ChIP-Seq]
we report that regional expression of the Hoxc genes is regulated by antagonistic switch between repression and activation epigenetic modification. In freshly isolated dermal cells from P50 telogen Wt/Wt ear skin, no enrichment of H3K27ac was detected at Hoxc cluster, consistent with their lack of expression; in contrast, robust peaks of this marker are observed in 3' region of the Hoxc cluster in dorsal skin dermal cells. Secondly we looked at H3K27 trimethylation (H3K27me3), a marker for polycomb-dependent gene repression, which antagonizes H3K27ac. Concomitantly, we found that H3K27me3 spread across the entire Hoxc cluster in adult ear skin dermal cells but was restricted to the 5' region of the Hoxc cluster in adult dorsal skin dermal cells . In adult dorsal skin dermal cells, we found three occupied CTCF binding sites inside Hoxc cluster. The rostral CTCF binding site marks the discontinuity point of H3K27me3 modification at the intergenic region between Hoxc11 and Hoxc10 in dorsal skin dermal cells. This indicates the CTCF binding event within Hoxc cluster might forge a topological barrier that can insulate activation region from repression region and therefore lead to the region specific expression of the Hoxc cluster genes.To directly test whether there is ectopic interaction between Hoxc cluster and the active domain in proximal-TAD, we used circularized chromosome conformation capture (4C) with Hoxc4 as bait. In Wt/Koa ear skin dermal cells, there are clear ectopic interactions of Hoxc4 with the remaining active regulatory landscape in proximal-TAD; on the other hand, all of the interactions of Hoxc4 remained inside the distal-TAD with repressive domain in Wt/Wt ear skin. Overall design: Examination of gene expression in wt/wt ear epidermal cells, wt/wt dorsal epidermal cells, and wt/koa ear epidermal  cells; Examination of gene expression and 2 histone modification in wt/wt ear dermal cells, wt/wt dorsal dermal cells, and wt/koa ear dermal cells; examination of CTCF binding in wt/wt ear dermal cells and wt/wt dorsal dermal cells; examination of chromatin interaction using Hoxc as viewpoint in wt/wt ear dermal cells and wt/koa ear dermal cells.