An optimization framework for unsupervised identification of rare copy number variation from SNP array data

Background

Specific chromatin characteristics, especially the modification status of the core histone proteins, are associated with active and inactive genes. There is growing evidence that genes that respond to environmental or developmental signals may possess distinct chromatin marks. Using a T cell model and both genome-wide and gene-focused approaches, we examined the chromatin characteristics of genes that respond to T cell activation.

Results

To facilitate comparison of genes with similar basal expression levels, we used expression-profiling data to bin genes according to their basal expression levels. We found that inducible genes in the lower basal expression bins, especially rapidly induced primary response genes, were more likely than their non-responsive counterparts to display the histone modifications of active genes, have RNA polymerase II (Pol II) at their promoters and show evidence of ongoing basal elongation. There was little or no evidence for the presence of active chromatin marks in the absence of promoter Pol II on these inducible genes. In addition, we identified a subgroup of genes with active promoter chromatin marks and promoter Pol II but no evidence of elongation. Following T cell activation, we find little evidence for a major shift in the active chromatin signature around inducible gene promoters but many genes recruit more Pol II and show increased evidence of elongation.

Conclusions

These results suggest that the majority of inducible genes are primed for activation by having an active chromatin signature and promoter Pol II with or without ongoing elongation.     

Defining the chromatin signature of inducible genes in T cells

Background

Specific chromatin characteristics, especially the modification status of the core histone proteins, are associated with active and inactive genes. There is growing evidence that genes that respond to environmental or developmental signals may possess distinct chromatin marks. Using a T cell model and both genome-wide and gene-focused approaches, we examined the chromatin characteristics of genes that respond to T cell activation.

Results

To facilitate comparison of genes with similar basal expression levels, we used expression-profiling data to bin genes according to their basal expression levels. We found that inducible genes in the lower basal expression bins, especially rapidly induced primary response genes, were more likely than their non-responsive counterparts to display the histone modifications of active genes, have RNA polymerase II (Pol II) at their promoters and show evidence of ongoing basal elongation. There was little or no evidence for the presence of active chromatin marks in the absence of promoter Pol II on these inducible genes. In addition, we identified a subgroup of genes with active promoter chromatin marks and promoter Pol II but no evidence of elongation. Following T cell activation, we find little evidence for a major shift in the active chromatin signature around inducible gene promoters but many genes recruit more Pol II and show increased evidence of elongation.

Conclusions

These results suggest that the majority of inducible genes are primed for activation by having an active chromatin signature and promoter Pol II with or without ongoing elongation.     

Cell-Extracellular Matrix Interactions in Normal and Diseased Skin

Mammalian skin comprises a multi-layered epithelium, the epidermis, and an underlying connective tissue, the dermis. The epidermal extracellular matrix is a basement membrane, whereas the dermal ECM comprises fibrillar collagens and associated proteins. There is considerable heterogeneity in ECM composition within both epidermis and dermis. The functional significance of this extends beyond cell adhesion to a range of cell autonomous and nonautonomous processes, including control of epidermal stem cell fate. In skin, cell-ECM interactions influence normal homeostasis, aging, wound healing, and disease. Disturbed integrin and ECM signaling contributes to both tumor formation and fibrosis. Strategies for manipulating cell-ECM interactions to repair skin defects and intervene in a variety of skin diseases hold promise for the future.The focus of this review is the role of cell-ECM interactions in the physiology of normal and diseased mammalian skin. The skin has epithelial and mesenchymal components and contains ECM comprising both fibrillar collagen and basement membrane. Experimentally, it is a highly tractable tissue, and a range of in vitro and in vivo approaches are available to explore cell-ECM interactions. Such studies are of medical importance because of the wide variety of benign and malignant skin diseases. Research on skin therefore provides an integrated, in vivo, context for understanding the functional significance of specific molecular interactions and signaling pathways involved in cell-ECM adhesion.     

Side population cells in human and mouse epidermis lack stem cell characteristics

Cells that exclude Hoechst 33342 have been found in many tissues, and common for these cells is a characteristic profile when analysed by flow fluorimetry (sp, side population). Since sp cells in some cases function as multipotent stem cells, we investigated whether the epidermis contains sp cells (Esp cells) and whether these cells were epidermal stem cells. We show that mouse and human epidermis contain sp cells, and, to identify the origin of these cells, we tested the expression of several marker genes. We find that Esp cells constitute a subpopulation of the alpha6 integrin-positive basal cells of the mouse epidermis. They are positive for sca-1 and negative for MHC class II and Flk1. They are not identical to the label-retaining population but are cycling cells in the mouse epidermis. Keratinocytes positive for sca-1 are located outside the stem cell containing bulge area of the mouse hair follicle. Forty-four human skin samples were analysed, and Esp cells were found at frequencies ranging from 0.01% to 5.39%, independently of age and body site. Human Esp cells did not express particular high levels of beta1 integrin. However, they expressed the half transporter ABCG2 and we identified high expression of this marker in the secretory duct epithelium of the sweat glands whereas low expression was found in the basal layer of the epidermis.     

Dolichos biflorus agglutinin-binding site expression in basal keratinocytes is associated with cell differentiation

A basal layer of squamous epithelia such as epidermis contains stem cells, transit amplifying cells as well as postmitotic differentiating cells. A detailed knowledge of the transition among these cell types in the course of epidermal renewal is important. It would help in better understanding of many pathological processes, including cancer, and in employment of epidermal cells for therapeutic purposes. In this study we analyzed the possible role of Dolichos biflorus agglutinin (DBA)-reactive alpha-N-acetylgalactosamine glycosylation in behavior of the human epidermal basal cells under in vivo and in vitro conditions. The data received from porcine epidermis were also included. Part of basal cells was positive for DBA-binding sites and these cells exhibited a lower presence of beta1 integrin in their basal surface connected to the basement membrane. The perinuclear Golgi-like accumulation of beta1 integrin was observed in some cultured keratinocytes. The co-localization of integrin with DBA-binding sites and 58 kDa protein suggests that alpha-N-acetylgalactosamine glycosylation could be related to beta1 integrin retention in the endoplasmatic reticulum Golgi intermediate compartment (ERGIC) at the beginning of the secretory pathway. The lack of anchorage in culture elevated the number of DBA-binding site positive cells without significant influence on cell growth when cells isolated directly from epidermis were employed in study. Some role of DBA-reactive glycoligand expressions in a suprabasal movement of differentiated basal cells can be hypothesized.