Physical Delineation of a 700-kb Region Overlapping theLooptailMutation on Mouse Chromosome 1

Abstract

The mouselooptail(Lp) mutation is an established model for neural tube defects with homozygousLpembryos showing an open neural tube from the caudal midbrain to the tip of the tail. HeterozygousLpmice are characterized by a “looped-tail” and wobbly head movements. TheLpgene has been mapped to a 0.6-cM interval on mouse chromosome 1 delineated by two clusters of markers,Fcer1γ/Usf1/D1Mit113/D1Wsu1on the proximal side andFcer1α/Spna1/D1Mit149distally. In the present study, we have created a high-resolution physical map of theLpgenetic interval that is based on long-range restriction mapping by PFGE, fluorescencein situhybridization analysis of interphase nuclei and extended chromatid fibers, and the assembly of a cloned contig. This contig consists of 25 independent and overlapping BAC clones and 3 YAC clones. The combined analysis indicates that the 0.6-cM genetic interval forLpcorresponds to a minimal physical interval of 700 kb that is delineated byD1Mit113proximally (two crossovers) andFcer1αdistally (one crossover). The overall gene order and intergene distances for the region were determined to beD1Mit113–<150 kb–Nhlh1–250 kb–Atp1α2–280 kb–Fcer1α. Partial sequencing of BAC clones from the contig yielded 42 new STS markers for this region of mouse chromosome 1. Sequence analysis of the BAC clones and assignment of ESTs from the human transcript map to the cloned contig allowed the placement of four new transcription units within this region:Pc326, Kiaa0253,andPea15were positioned in theNhlh1/Atp1α2nonrecombinant interval, whileGirk3was located distal toAtp1α2.