Physical delineation of a 700-kb region overlapping the looptail mutation on mouse chromosome 1

The mouse looptail (Lp) mutation is an established model for neural tube defects with homozygous Lp embryos showing an open neural tube from the caudal midbrain to the tip of the tail. Heterozygous Lp mice are characterized by a "looped-tail" and wobbly head movements. The Lp gene has been mapped to a 0.6-cM. interval on mouse chromosome 1 delineated by two clusters of markers, Fcer1 gamma/Usf1/D1Mit113/D1Wsu1 on the proximal side and Fcer1 alpha/Spna1/D1Mit149 distally. In the present study, we have created a high-resolution physical map of the Lp genetic interval that is based on long-range restriction mapping by PFGE, fluorescence in situ hybridization 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 for Lp corresponds to a minimal physical interval of 700 kb that is delineated by D1Mit113 proximally (two crossovers) and Fcer1 alpha distally tone crossover). The overall gene order and intergene distances for the region were determined to be D1Mit113-<150 kb-Nhlh1-250 kb-Atp1 alpha 2-280 kb-Fcer1 alpha. 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, and Pea15 were positioned in the Nhlh1/Atp1 alpha 2 nonrecombinant interval, while Girk3 was located distal to Atp1 alpha 2. (C) 1999 Academic Press.