STRUCTURAL-ANALYSIS OF PAX3 GENOMIC REARRANGEMENTS IN ALVEOLAR RHABDOMYOSARCOMA

In the pediatric cancer alveolar rhabdomyosarcoma, the (2;13)(q35;q14) translocation juxtaposes PAX3 and FKHR to produce a chimeric PAX3-FKH R gene. With the use of Southern blot methodology, genomic rearrangeme nts of PAX3 intron 7 were detected in 23 of 23 fusion-positive alveola r rhabdomyosarcomas and were not detected in 19 fusion-negative embryo nal rhabdomyosarcomas. Rearrangements corresponding to the reciprocal FKHR-PAX3 fusion were detected in 21 of 23 PAX3-FKHR-positive cases, t hough FKHR-PAX3 transcripts were detected in only 15 of 23 cases. Mapp ing experiments demonstrated that breakpoints occurred throughout this 17.5 kb PAX3 intron and, in 12 of 23 cases, breakpoints clustered wit hin a 4.5-kb region at the 3' end of the intron. Chromatin analysis re vealed a prominent DNase I hypersensitive site at the 5' end of the in tron but did not indicate any other DNA-protein interactions that migh t have affected the breakpoint distribution. Sequence analysis identif ied AT-rich regions within the 3' cluster, as well as alternating puri ne-pyrimidine and homopyrimidine elements at the borders of this clust er. These finding suggest that translocation breakpoints are constrain ed to PAX3 intron 7 primarily by functional boundaries related to the flanking exons and may be secondarily affected by sequence features wi thin this intron. (C) Elsevier Science Inc., 1998.