South, Andrew P.; (1999) Construction of an integrated map of the genomic locus 1q21 harboring the human epidermal differentiation complex as a platform for the identification of all genes in this complex, the study of their expression, regulation, function and evolution. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

The human Epidermal Differentiation Complex (EDC) on chromosome 1q21 consists of three structurally different, yet functionally related, gene families. Members of all three gene families have been shown to play important roles in epidermal differentiation. This thesis initially describes the assembly of a completely contiguous set of overlapping bacterial clones covering 2.45Mb of human genomic DNA from the 1q21 locus, encompassing the entire EDC. All known genes (28) and eight DNA markers within the EDC are precisely localized to EcoRI restriction enzyme fragments that constitute a partial EcoRI and full NotI and SalI restriction enzyme map. The bacterial clones presented in this thesis have been accepted as the substrate for long range genomic sequencing of this region for the chromosome 1 sequencing project at the Sanger Centre, UK. In addition to providing a template for large-scale sequencing, the bacterial clones presented here will serve as a molecular resource for the elucidation of all transcripts within the EDC as well as the study of transcriptional regulation, function and evolution of the EDC. As an evaluation of this resource as a tool for the identification of transcribed sequences, exon trapping has been performed from three PAC clones. The exon trapping experiments described in this thesis have identified 13 putative exons that are shown to derive from the EDC. Searches of the publicly available databases with the sequences of these 13 putative exons have identified a novel cDNA clone that is shown to localize to the EDC. Two of the thirteen putative exons identified are homologous, but not identical, to this novel cDNA. These data coupled with Northern blot and RT-PCR analysis, suggests that yet another novel family of transcribed sequences has been identified within the EDC. Thirteen gene members of the S100 family of calcium binding proteins constitute one of the three so-far identified multi-gene families residing in the EDC. By using the contiguous bacterial clone map towards the study of EDC evolution, two findings have been made. Firstly, evidence of an ancestral break-point inversion during the evolution of mammals is supported by the elucidation of the transcriptional orientation of four S100 genes and by the identification of extensive alternative splicing of the 5' untranslated region of one of these S100 genes. Secondly, a similar clustering of S100 genes to that seen in human and mouse is described for the first non-mammalian vertebrate species, Gallus gallus.

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