A splice defect in the EDA gene in dogs with an X-linked ectodermal dysplasia. EDA-RNAseq

X-linked hypohidrotic ectodermal dysplasia (XLHED) caused by variants in the EDA gene represents the most common ectodermal dysplasia in humans. We investigated three male mixed-breed dogs with an ectodermal dysplasia phenotype characterized by marked hypotrichosis, absence of sweat glands and altered dentition with missing and abnormally shaped teeth. Analysis of whole genome sequence data from the three affected dogs and 281 control dogs revealed that the affected dogs shared the same haplotype on a large segment of the X-chromosome, whereas they did not share any large homozygous segments elsewhere in the genome. Unexpectedly, bioinformatic analysis of the sequence data did not reveal any private non-synonymous variant in the affected dogs within the shared haplotype on the X chromosome. Furthermore, no private DNA variants were found in the EDA gene. We therefore performed an RNA-seq experiment on skin biopsies to search for changes in the transcriptome. This analysis revealed that the EDA transcript in the affected dogs lacked 103 nucleotides encoded by exon 2. We speculate that this exon skipping is caused by a genetic variant located in one of the large introns flanking this exon, which was missed by whole genome sequencing with the illumina short read technology. The altered EDA transcript splicing most likely causes the observed XLHED in the affected dogs. These dogs thus offer an excellent opportunity to gain insights into the complex splicing processes required for expression of the EDA gene and other genes with large introns.