The keratins are highly specific epithelial intermediate filaments family included 54 genes clustered at two different chromosomal sites: locus 17q21.2 contains type I keratin genes, and locus 12q13.13 contains type II keratin genes and K18. Keratins expression pattern depends on epithelial type and differentiation stage and could characterize the pathologic conditions like wound healing or cancer progression. Lineage-specific expression profile is regulated by microenvironment signaling that alters epigenetic landscape of keratin loci. We applied the novel high-resolution chromosome conformation capture method, C-TALE (Chromatin TArget Ligation Enrichment) to obtain the heatmap of the spatial chromatin organization of 12q13.13 locus during the human epidermal skin keratinocyte differentiation. We identified two regions with potential enhancer activity. In basal epidermal K5/K14 positive keratinocytes both regions formed spatial contact with the keratin 5 gene and lost it in spinous K1/K10 keratinocytes while the interactions between the keratin 1 gene and regions of interests increased. In both keratinocyte subtypes the studied regions contacted to each other and isolated a significant part of the locus in an extended chromatin loop. Epigenetic profiles from the ENCODE database revealed the high level of H3K27ac, H3K4me, DNAse I hypersensitivity sites, several transcription factors binding motifs (KLF6, SP1, THAP1, AP2) and CTCF-binding sites in both regions, that denote these regions of interest as a potential major regulatory element.
The work was performed according to IDB RAS Basic Researcher Program No0108-­2019-­0004.

Identifying the regulatory elements at the keratin type I and II locus 12q13.13 using C-TALE method during human epidermal skin keratinocytes differentiation