Research
My major research interests are chromatin dynamics and gene regulation in skin morphogenesis, homeostasis and regeneration. Specifically my research focuses on how 3D genome organization, higher order chromatin folding, ATP-dependent chromatin remodelling and covalent DNA modifications are involved in the transcription regulation in epithelial progenitor cell (PC) homeostasis and differentiation. The skin represents a very attractive model to study genetic and epigenetic mechanisms of gene regulation in adult PCs in dynamic self-renewing tissue. Recently we have shown the remarkable higher-order chromatin remodelling of Epidermal Differentiation Complex locus (EDC), containing many genes encoding proteins essential for epidermal keratinocyte differentiation and barrier formation, in epidermal PCs during murine skin morphogenesis. In particular, we demonstrated de-condensation and relocation of the EDC locus towards the nuclear interior in epidermal basal keratinocytes upon onset of epidermal stratification between 11.5 days of gestation (E 11.5) and E16.5, using 3D FISH analysis of spatially preserved nuclei in mouse embryonic skin. Importantly, the numerous genes within EDC are moderately up-regulated in basal keratinocytes at E16.5 in comparison to E11.5. Some of the genes are further significantly up-regulated in suprabasal keratinocytes. The remodelling of the higher-order chromatin structure within EDC was essentially completed in basal keratinocytes at E16.5 at least at the resolution provided by the 3D FISH analysis. This suggests that such remodelling is required for high levels of expression of some EDC genes in differentiating suprabasal keratinocytes. The relocation of EDC towards the nuclear interior is a locus-specific and is not associated with the inter-nuclear relocation of the EDC containing chromosome territory 3 or constitutively highly expressed genes located within 1Mb neighbourhood of the locus (Mardaryev et al, Development, 2014) We have also demonstrated that p63 transcriptional master regulator of epidermal development is essential for the higher order chromatin remodelling within EDC (Fessing et al, J Cell Biology, 2011, Mardaryev et al, Development 2014). Importantly, a set of genes encoding chromatin structural proteins and remodellers were down-regulated in p63 deficient mouse epidermis, including genome organizer Satb1 and ATP-dependent chromatin remodeller Brg1/Smarca4. We showed that Satb1 and Brg1 are direct transcriptional targets for p63 and EDC higher-order chromatin structure and gene expression profile is significantly altered in Satb1 or Brg1 deficient epidermis. Importantly, Satb1 and Brg1 directly bind to the specific genomic regions within EDC. In spite of recent progress in stem cell biology, our knowledge of epigenetic mechanisms governing their homeostasis and differentiation in vivo remains very limited. Moreover, the mechanisms controlling the coordinated gene regulation within loci of tissue-specific genes, including EDC, during epithelial PC differentiation in epidermis and hair follicle are mostly unexplored. The long-term goals of my research are: 1) To define fundamental principles of 3D genome organization and mechanisms controlling its establishment and remodelling in mammals using skin epithelium as a model system 2) To identify how ATP dependent chromatin remodellers control gene expression programmes in skin epithelial stem cells and their progeny during skin and hair follicle regeneration and ageing 3) To identify how 5-methylcytosine oxidation in DNA and Tet proteins control gene expression programmes in skin epithelial stem cells and their progeny during skin development, homeostasis, regeneration and ageing. Chromatin remodelling processes in human hair growth cycle and impact of chronological ageing on chromatin remodelling in hair regeneration DNA hydroxymethylation, TET enzymes and regulation of stem cell activity during skin regeneration and wound healing Higher-order chromatin remodelling and 3D genome organization in skin development and regeneration Prof Vladimir Botchkarev (University of Bradford) Prof Job Dekker (University of Massachusetts School of Medicine, Worcester, MA, USA) Prof Wolf Reik (Babraham Institute, Cambridge, UK)
