Sequence analysis of a radiation-induced deletion breakpoint fusion in mouse

Abstract

C l lDSD is an X-ray-induced deletion generated at the Oak Ridge National Laboratory (Russell et al. 1979) that spans ~3 cM (Sharan et al. 1991) of mouse Chromosome (Chr) 7 including the c (albino) locus. The c11DSD-deletion breakpoint fusion fragment was cloned from a C3H/101 background (Sharan et al. 1991). Clones from a wild-type 129/SV phage genomic library (Stratagene) corresponding to the proximal and distal breakpoints of the deletion were isolated. The cHDSD-breakpoint fusion fragment and wildtype clones were sequenced and compared. The purpose was to determine whether any flanking rearrangements and/or sequence motifs were associated with the fusion site. Sequence flanking the cllDSD-breakpoint fusion was aligned with the wild-type proximal and distal sequences (Fig. 1). Homology between the C l lDSD and proximal wildtype sequence ends at the fusion site, after which homology between the distal wild-type and c 11DsD sequences begins (Fig. 1). The exact fusion site could not be determined because of a two-base overlap marked by the box in Fig. 1. A single base mismatch was present in both homologous proximal and distal sequences, and these are probably the result of polymorphism between strains. No significant sequence homology was found between the proximal and distal sides of the fusion. A BLASTN (Altschul et al. 1990) search showed the proximal side to be ~80% homologous to rat (Bilofsky and Burks 1988) and mouse (Shehee et al. 1987) long interspersed elements (LINEs), whereas the distal side showed no homology matches. This breakpoint fusion sequence in context with two other sequenced radiation-induced breakpoint fusions, pCp (Nakatsuet al. 1993) and Aa2 (Strobel et al. 1990), illustrates the precise nature with which induced double-strand breaks can be joined.