The transcription in the eukaryotic cells involves epigenetic regulatory mechanisms that control local and higher-order chromatin remodelling. In the skin, keratinocyte-specific genes are organized into distinct loci including Epidermal Differentiation Complex (EDC) and Keratin type I/II loci. This thesis introduces bioinformatics approaches to analyze multi-level regulatory mechanisms that control skin development and keratinocyte-specific differentiation. Firstly, integration of gene expression data with analyses of linear genome organization showed dramatic downregulation of the genes that comprise large genomic domains in the sweat glands including EDC locus, compared to ii hair follicles, suggesting substantial differences in global genome rearrangement during development of these two distinct skin appendages. Secondly, comparative analysis of the genetic programmes regulated in keratinocytes by Lhx2 transcription factor and chromatin remodeler Satb1 revealed that significant number of their target genes is clustered in the genome. Furthermore, it was shown in this study that Satb1 target genes are lineage-specific. Thirdly, analysis of the topological interactomes of Loricrin and Keratin 5 in hair follicle steam cells revealed presence of the cis- and trans-interactions and lineage specific genes (Wnt, TGF-beta/activin, Notch, etc.). Expression levels of the genes that comprise interactomes show correlation with their histone modification status. This study demonstrates the crucial role for integration of transcription factormediated and epigenetic regulatory mechanisms in establishing a proper balance of gene expression in keratinocytes during development and differentiation into distinct cell lineages and provides an integrated bioinformatics platform for further analyses of the changes in global organization of keratinocyte-specific genomic loci in normal and diseased skin.

La peau est un organe qui enveloppe le corps, elle est une barrière naturelle importante et efficace contre différents envahisseurs. Pour le traitement des maladies dermatologiques ainsi que dans l'industrie cosmétique, les applications topiques sur la peau sont largement utilisées. Ainsi beaucoup d'efforts ont été investis dans la recherche sur la peau visant à comprendre l'absorption moléculaire et les mécanismes rendant efficace la pénétration. Cependant, il reste difficile d'obtenir une visualisation 3D de haute résolution combinée à une information chimique- ment spécifique et quantitative dans la recherche sur la peau. La spectroscopie et la microscopie non-linéaire, incluant la fluorescence excitée à 2-photon (TPEF), la diffusion Raman spontanée, la diffusion Raman cohérente anti-Stokes (CARS) et la diffusion Raman stimulée (SRS), sont introduits dans ce travail pour l'identification sans ambiguïté de la morphologique de la peau et la détection de molécules appliquées de façon topique. Plusieurs méthodes quantitatives basées sur la spectroscopie et la microscopie non-linéaire sont proposées pour l'analyse chimique en3D sur la peau artificielle, ex vivo et in vivo sur la peau humaine. De plus, afin de s'adapter aux applications cliniques à venir, un design endoscopique est étudié pour permettre l'imagerie non-linéaires dans les endoscopes flexibles. / Skin is an organ that envelops the entire body, acts as a pivotal, efficient natural barrier to- wards various invaders. For the treatment of major dermatological diseases and in the cosmetic industry, topical applications on skin are widely used, thus many efforts in skin research have been aimed at understanding detailed molecular absorption and efficient penetration mechanisms. However, it remains difficult to obtain high-resolution visualization in 3D together with chemical selectivity and quantification in skin research. Nonlinear spectroscopy and microscopy, including two-photon excited fluorescence (TPEF), spontaneous Raman scattering, coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS), are introduced in this work for unambiguous skin morphological identification and topical applied molecules detection. Sev- eral quantitative methods based on nonlinear spectroscopy and microscopy are designed for 3D chemical analysis in reconstructed skin, ex vivo and in vivo on human skin. Furthermore, to adapt to forthcoming clinical applications, an endoscopic design is investigated to bring nonlin- ear imaging in flexible endoscopes.

The transcription in the eukaryotic cells involves epigenetic regulatory mechanisms that control local and higher-order chromatin remodelling. In the skin, keratinocyte-specific genes are organized into distinct loci including Epidermal Differentiation Complex (EDC) and Keratin type I/II loci. This thesis introduces bioinformatics approaches to analyze multi-level regulatory mechanisms that control skin development and keratinocyte-specific differentiation. Firstly, integration of gene expression data with analyses of linear genome organization showed dramatic downregulation of the genes that comprise large genomic domains in the sweat glands including EDC locus, compared to ii hair follicles, suggesting substantial differences in global genome rearrangement during development of these two distinct skin appendages. Secondly, comparative analysis of the genetic programmes regulated in keratinocytes by Lhx2 transcription factor and chromatin remodeler Satb1 revealed that significant number of their target genes is clustered in the genome. Furthermore, it was shown in this study that Satb1 target genes are lineage-specific. Thirdly, analysis of the topological interactomes of Loricrin and Keratin 5 in hair follicle steam cells revealed presence of the cis- and trans-interactions and lineage specific genes (Wnt, TGF-beta/activin, Notch, etc.). Expression levels of the genes that comprise interactomes show correlation with their histone modification status. This study demonstrates the crucial role for integration of transcription factormediated and epigenetic regulatory mechanisms in establishing a proper balance of gene expression in keratinocytes during development and differentiation into distinct cell lineages and provides an integrated bioinformatics platform for further analyses of the changes in global organization of keratinocyte-specific genomic loci in normal and diseased skin.