Next-Generation Sequencing Identifies the Danforth's Short Tail Mouse Mutation as a Retrotransposon Insertion Affecting <em>Ptf1a</em> Expression

<div><p>The semidominant Danforth's short tail (<i>Sd</i>) mutation arose spontaneously in the 1920s. The homozygous <i>Sd</i> phenotype includes severe malformations of the axial skeleton with an absent tail, kidney agenesis, anal atresia, and persistent cloaca. The <i>Sd</i> mutant phenotype mirrors features seen in human caudal malformation syndromes including urorectal septum malformation, caudal regression, VACTERL association, and persistent cloaca. The <i>Sd</i> mutation was previously mapped to a 0.9 cM region on mouse chromosome 2qA3. We performed Sanger sequencing of exons and intron/exon boundaries mapping to the <i>Sd</i> critical region and did not identify any mutations. We then performed DNA enrichment/capture followed by next-generation sequencing (NGS) of the critical genomic region. Standard bioinformatic analysis of paired-end sequence data did not reveal any causative mutations. Interrogation of reads that had been discarded because only a single end mapped correctly to the <i>Sd</i> locus identified an early transposon (ETn) retroviral insertion at the <i>Sd</i> locus, located 12.5 kb upstream of the <i>Ptf1a</i> gene. We show that <i>Ptf1a</i> expression is significantly upregulated in <i>Sd</i> mutant embryos at E9.5. The identification of the <i>Sd</i> mutation will lead to improved understanding of the developmental pathways that are misregulated in human caudal malformation syndromes.</p>