GENOMIC ORGANIZATION OF THE HUMAN PAX3 GENE - DNA-SEQUENCE ANALYSIS OF THE REGION DISRUPTED IN ALVEOLAR RHABDOMYOSARCOMA

Mutations in the human PAX3 gene have previously been associated with two distinct diseases, Waardenburg syndrome and alveolar rhabdomyosarc oma. In this report we establish that the normal human PAX3 gene is en coded by 8 exons. Intron-exon boundary sequences were obtained for PAX 3 exons 5, 6, 7, and 8 and together with previous work provide the com plete genomic sequence organization for PAX3. Difficulties in obtainin g overlapping genomic clone coverage of PAX3 were circumvented in part by RARE cleavage mapping, which showed that the entire PAX3 gene span s 100 kb of chromosome 2. Sequence analysis of the last intron of PAX3 , which contains the previously mapped t(2;13)(q35;q14) translocation breakpoints of alveolar rhabdomyosarcoma, revealed the presence of a p air of inverted Alu repeats and a pair of inverted (GT)(n)-rich micros atellite repeats within a 5-kb region. This work establishes the compl ete structure of PAX3 and will permit high-resolution analyses of this locus for mutations associated with Waardenburg syndrome, alveolar rh abdomyosarcoma, and other phenotypes for which PAX3 may be a candidate locus. (C) 1995 Academic Press, Inc.