Positional Cloning of cobblestone, a Mouse Mutant Showing Major Defects in Brain Development, Identifies Ift88 as a Candidate Gene

The ENU-induced cobblestone (cbs) mouse mutant exhibits severe defects in fore- and midbrain development. Via genomic mapping, the causative mutation for the cbs-phenotype has previously been located on chromosome 14 in the proximity of the gene Ift88 (Intraflagellar transport, 88 kDa). The Ift88 protein is involved in intraflagellar transport and is required for genesis and maintenance of primary and motile cilia. In order to refine the genetic interval further, we performed fine-mapping analysis of the cbs mutant. The candidate region of the cbs mutation is shown to be situated in a region of 4.14 Mb on chromosome 14, containing the Ift88 gene, and excluding dozens of genes present in the roughly-mapped interval. However, neither sequencing of the core Ift88 promoter region nor of two conserved intronic sequences within Ift88 revealed any mutations, indicating that the responsible mutation lies in a transcriptional regulatory sequence within or near the Ift88 gene. Finally, other potential candidate genes in this genetic interval have been identified using synteny analysis on six other vertebrate genomes. This analysis is thus compatible with the idea that the mutation in cbs is located on the Ift88 gene, but it also allows the possibility of other candidate genes that lie near Ift88 to be involved in the phenotype.