Genome annotation of the 1.2MB Region on chromosome 8p22-p23.1 harbouring the gene for Keratolytic Winter Erythema (KWE)
Date
2012-01-17
Authors
Aron, Shaun Lyle
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Abstract
Keratolytic winter erythema (KWE) or Oudtshoorn skin disease is a rare autosomal dominant skin disorder for which the genetic cause remains unknown. The disorder manifests in the form of erythema and hyperkeratosis of the palmar-plantar regions and has been linked to a 1.2Mb region on chromosome 8p22-23.1 between markers D8S1759 and D8S552. A prevalence of 1/7200 has been observed in the South African Afrikaans-speaking white population with a lower unspecified prevalence occurring in the coloured South African population. A number of positional candidate genes within the critical region have been assessed for pathogenic mutations, however to date the causative gene has not been identified.
The objective of the current study was to examine the KWE critical region for highly conserved coding and non-coding regions and copy number variants (CNV) and to determine if these regions may play a role in the molecular etiology of the disease. Highly conserved regions were identified based on sequence conservation across a range of evolutionary diverse organisms. These regions were further analysed for possible protein-coding gene structure, regulatory motifs and RNA secondary structure. In addition, a custom CGH tiling array (384K Roche-Nimblegen) was used to identify CNVs across the extended KWE critical region in both affected and unaffected individuals. The multi-species sequence alignment revealed eight regions that showed a high level of conservation above a 70% threshold. Functional analysis of two of the conserved regions led to the identification of a novel protein-coding gene deubiquitinating enzyme 3 (DUB3) within the critical region which presented as a credible functional candidate for KWE. Two of the conserved regions were identified within an open reading frame c8orf13 which has previously been examined and found to contain no pathogenic mutations that segregate with the KWE phenotype. The remaining four highly conserved regions were found within non-coding sequence and computational analysis revealed putative regulatory motifs in the form of transcription factor binding sites. The copy number variation analysis did not show evidence for the presence of any large or small consistent CNV alleles likely to impact on any of the functional candidate genes in the KWE critical region. No common CNV alleles were observed in all of the KWE affected individuals examined and showed absence in unaffected family members. A significant variation in copy number was however observed in affected individuals within a previously defined copy number variable beta-defensin gene cluster which has been associated with psoriasis. Although the exact copy number of the cluster could not be determined in the present study due to the cross hybridization between genes in the family, the CNV observed in affect individuals for the cluster suggests that it may be involved in the modulation of the clinical severity of KWE.
The present study has led to the identification of a previously uncharacterised novel gene DUB3 within the KWE critical region which furthermore presented as a plausible functional candidate for the KWE phenotype. In addition, it has revealed that the molecular cause of KWE is unlikely to be exclusively due to copy number variation within the genes in the critical region. The current study has provided valuable insight into the KWE linked critical region and revealed a number of potential regions of interest to be examined in further studies exploring the molecular cause of the disease.