SEQUENCE-ANALYSIS OF THE BREAKPOINT REGIONS OF AN X-5 TRANSLOCATION IN A FEMALE WITH DUCHENNE MUSCULAR-DYSTROPHY

X;autosome translocations in females with Duchenne muscular dystrophy (DMD) provide an opportunity to study the mechanisms responsible for c hromosomal rearrangements that occur in the germ line. We describe her e a detailed molecular analysis of the translocation breakpoints of an X;autosome reciprocal translocation, t(X;5)(p21;q31.1), in a female w ith DMD. Cosmid clones that contained the X-chromosome breakpoint regi on were identified, and subclones that hybridized to the translocation junction fragment in restriction digests of the patient's DNA were is olated and sequenced. Primers designed from the X-chromosomal sequence were used to obtain the junction fragments on the der(X) and the der( 5) by inverse PCR. The resultant clones were also cloned and sequenced , and this information used to isolate the chromosome 5 breakpoint reg ion. Comparison of the DNA sequences of the junction fragments with th ose of the breakpoint regions on chromosomes X and 5 revealed that the translocation arose by nonhomologous recombination with an imprecise reciprocal exchange. Four and six base pairs of unknown origin are ins erted at the exchange points of the der(X) and der(5), respectively, a nd three nucleotides are deleted from the X-chromosome sequence. Two f eatures were found that may have played a role in the generation of th e translocation. These were (1) a repeat motif with an internal homopy rimidine stretch 10 bp upstream from the X-chromosome breakpoint and ( 2) a 9-bp sequence of 78% homology located near the breakpoints on chr omosomes 5 and X.