title: Dynamic and physical clustering of gene expression during epidermal barrier formation in differentiating keratinocytes.
abstract: The mammalian epidermis is a continually renewing structure that provides the interface between the organism and an innately hostile environment. The keratinocyte is its principal cell. Keratinocyte proteins form a physical epithelial barrier, protect against microbial damage, and prepare immune responses to danger. Epithelial immunity is disordered in many common diseases and disordered epithelial differentiation underlies many cancers. In order to identify the genes that mediate epithelial development we used a tissue model of the skin derived from primary human keratinocytes. We measured global gene expression in triplicate at five times over the ten days that the keratinocytes took to fully differentiate. We identified 1282 gene transcripts that significantly changed during differentiation (false discovery rate <0.01%). We robustly grouped these transcripts by K-means clustering into modules with distinct temporal expression patterns, shared regulatory motifs, and biological functions. We found a striking cluster of late expressed genes that form the structural and innate immune defences of the epithelial barrier. Gene Ontology analyses showed that undifferentiated keratinocytes were characterised by genes for motility and the adaptive immune response. We systematically identified calcium-binding genes, which may operate with the epidermal calcium gradient to control keratinocyte division during skin repair. The results provide multiple novel insights into keratinocyte biology, in particular providing a comprehensive list of known and previously unrecognised major components of the epidermal barrier. The findings provide a reference for subsequent understanding of how the barrier functions in health and disease.
authors.affiliation: Wellcome Trust Centre for Human Genetics, Oxford, England.
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Taylor
authors.forename: Teresa L
authors.initials: TL
authors.lastname: Street
authors.forename: Lizhong
authors.initials: L
authors.lastname: Hao
authors.forename: Richard
authors.initials: R
authors.lastname: Copley
authors.forename: Martin S
authors.initials: MS
authors.lastname: Taylor
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Hayden
authors.forename: Gina
authors.initials: G
authors.lastname: Stolper
authors.forename: Richard
authors.initials: R
authors.lastname: Mott
authors.forename: Jotun
authors.initials: J
authors.lastname: Hein
authors.forename: Miriam F
authors.initials: MF
authors.lastname: Moffatt
authors.forename: William O C M
authors.initials: WO
authors.lastname: Cookson
mesh_terms: D000465:Algorithms; D002454:Cell Differentiation; D016000:Cluster Analysis; D000078404:Epidermal Cells; D005189:False Positive Reactions; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D007107:Immune System; D015603:Keratinocytes / Q000166:cytology*; D008954:Models, Biological; D005810:Multigene Family; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic