The epidermal differentiation complex (EDC) encodes co-ordinately regulated genes critically involved in epidermal differentiation, however knowledge of the molecular mechanisms involved in co-ordinating EDC gene expression is limited. Recent findings indicate p63 dependent changes in the nuclear localisation and higher-order chromatin folding the EDC coincide with the onset of epidermal stratification during embryonic development. Here it is demonstrated that a direct transcription target of p63, the chromatin-remodelling enzyme Brg1, modulates the specific nuclear positioning of the EDC and transcription of differentiation-specific gene encoded at the EDC. In addition, the results of high-resolution 5C-based analyses of the spatial chromatin interactome at a 5.3Mb region spanning the murine EDC in epidermal keratinocytes, and the silenced EDC in thymocytes, are presented. Chromatin interactions at the EDC region in keratinocytes include long-range interactions between multiple proximal and distal candidate gene regulatory regions. Many candidate regulatory elements involved in looping chromatin interactions at the EDC region are enriched for both active (H3K4me1, H3K27ac) and repressive (H3K27me3) chromatin marks and are bound by Sin3a and RBP2 co-repressor complexes. The chromatin interactome at the EDC in epidermal progenitor cells is enriched for bound chromatin architectural proteins Satb1, Satb2, and the cohesin subunit Rad21. Further, a substantial degree of co-localisation is observed between these chromatin architectural proteins, transcription factors and co-factors. Findings presented here suggest that a functional chromatin interactome, mediated by Satb proteins and cohesin, acts in conjunction with transcriptional repressor complexes to facilitate co-ordinated gene expression at the EDC in epidermal progenitor cells upon differentiation. These results provide a foundation for further study of the mechanisms controlling EDC gene expression in health and disease.

The epidermal differentiation complex (EDC) encodes co-ordinately regulated genes critically involved in epidermal differentiation, however knowledge of the molecular mechanisms involved in co-ordinating EDC gene expression is limited. Recent findings indicate p63 dependent changes in the nuclear localisation and higher-order chromatin folding the EDC coincide with the onset of epidermal stratification during embryonic development. Here it is demonstrated that a direct transcription target of p63, the chromatin-remodelling enzyme Brg1, modulates the specific nuclear positioning of the EDC and transcription of differentiation-specific gene encoded at the EDC. In addition, the results of high-resolution 5C-based analyses of the spatial chromatin interactome at a 5.3Mb region spanning the murine EDC in epidermal keratinocytes, and the silenced EDC in thymocytes, are presented. Chromatin interactions at the EDC region in keratinocytes include long-range interactions between multiple proximal and distal candidate gene regulatory regions. Many candidate regulatory elements involved in looping chromatin interactions at the EDC region are enriched for both active (H3K4me1, H3K27ac) and repressive (H3K27me3) chromatin marks and are bound by Sin3a and RBP2 co-repressor complexes. The chromatin interactome at the EDC in epidermal progenitor cells is enriched for bound chromatin architectural proteins Satb1, Satb2, and the cohesin subunit Rad21. Further, a substantial degree of co-localisation is observed between these chromatin architectural proteins, transcription factors and co-factors. Findings presented here suggest that a functional chromatin interactome, mediated by Satb proteins and cohesin, acts in conjunction with transcriptional repressor complexes to facilitate co-ordinated gene expression at the EDC in epidermal progenitor cells upon differentiation. These results provide a foundation for further study of the mechanisms controlling EDC gene expression in health and disease.

Yes / Mammalian genomes contain several dozens of large (>0.5 Mbp) lineage-specific gene loci harbouring functionally related genes. However, spatial chromatin folding, organization of the enhancer-promoter networks and their relevance to Topologically Associating Domains (TADs) in these loci remain poorly understood. TADs are principle units of the genome folding and represents the DNA regions within which DNA interacts more frequently and less frequently across the TAD boundary. Here, we used Chromatin Conformation Capture Carbon Copy (5C) technology to characterize spatial chromatin interaction network in the 3.1 Mb Epidermal Differentiation Complex (EDC) locus harbouring 61 functionally related genes that show lineage-specific activation during terminal keratinocyte differentiation in the epidermis. 5C data validated by 3D-FISH demonstrate that the EDC locus is organized into several TADs showing distinct lineage-specific chromatin interaction networks based on their transcription activity and the gene-rich or gene-poor status. Correlation of the 5C results with genome-wide studies for enhancer-specific histone modifications (H3K4me1 and H3K27ac) revealed that the majority of spatial chromatin interactions that involves the gene-rich TADs at the EDC locus in keratinocytes include both intra- and inter-TAD interaction networks, connecting gene promoters and enhancers. Compared to thymocytes in which the EDC locus is mostly transcriptionally inactive, these interactions were found to be keratinocyte-specific. In keratinocytes, the promoter-enhancer anchoring regions in the gene-rich transcriptionally active TADs are enriched for the binding of chromatin architectural proteins CTCF, Rad21 and chromatin remodeler Brg1. In contrast to gene-rich TADs, gene-poor TADs show preferential spatial contacts with each other, do not contain active enhancers and show decreased binding of CTCF, Rad21 and Brg1 in keratinocytes. Thus, spatial interactions between gene promoters and enhancers at the multi-TAD EDC locus in skin epithelial cells are cell type-specific and involve extensive contacts within TADs as well as between different gene-rich TADs, forming the framework for lineage-specific transcription. / This study was supported by the grants 5R01AR064580 and 1RO1AR071727 to VAB, TKS and AAS, as well as by the grants from MRC (MR/ M010015/1) and BBSRC (BB/K010050/1) to VAB.