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

Christopher N Vlangos,James D Cavalcoli,Robert H Lyons,Amanda N Siuniak,Arul M Chinnaiyan,Dan Robinson,Catherine E Keegan,Wayne N Frankel

doi:10.1371/journal.pgen.1003205

Christopher N Vlangos, James D Cavalcoli + Show 6 more

Open Access

https://doi.org/10.1371/journal.pgen.1003205

Copy DOI

Abstract

The semidominant Danforth's short tail (Sd) mutation arose spontaneously in the 1920s. The homozygous Sd phenotype includes severe malformations of the axial skeleton with an absent tail, kidney agenesis, anal atresia, and persistent cloaca. The Sd mutant phenotype mirrors features seen in human caudal malformation syndromes including urorectal septum malformation, caudal regression, VACTERL association, and persistent cloaca. The Sd 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 Sd 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 Sd locus identified an early transposon (ETn) retroviral insertion at the Sd locus, located 12.5 kb upstream of the Ptf1a gene. We show that Ptf1a expression is significantly upregulated in Sd mutant embryos at E9.5. The identification of the Sd mutation will lead to improved understanding of the developmental pathways that are misregulated in human caudal malformation syndromes.

Highlights

The Danforth’s short tail (Sd) mouse mutation arose spontaneously in the early 1920s in an inbred mouse colony maintained in the laboratory of C.H
Little is known regarding the genetic causes of human caudal birth defects
We used next-generation sequencing to identify the genetic cause of the Sd mouse phenotype

Summary

Introduction

The Danforth’s short tail (Sd) mouse mutation arose spontaneously in the early 1920s in an inbred mouse colony maintained in the laboratory of C.H. Danforth [1,2]. The inbred line in which the Sd mutation arose was being maintained for study of a dominant but incompletely penetrant posterior duplication phenotype. Danforth shared four mice with shortened tails (2 males and 2 females) with L.C. Dunn and S. None of the offspring of these shared mice displayed the posterior duplication phenotype, indicating that Danforth’s original line was segregating two different mutations [1,2]. The new short tailed line was named short-Danforth or Sd. Dunn et al determined that the Sd mutation was inherited in a semi-dominant manner with complete penetrance and was not allelic to Brachyury (T) [2]

Methods

Results

Discussion

Conclusion