Barr F G, Nauta L E, Hollows J C
Department of Pathology, University of Pennsylvania School of Medicine, Philadelphia 19104-6082, USA.
Cancer Genet Cytogenet. 1998 Apr 1;102(1):32-9. doi: 10.1016/s0165-4608(97)00287-2.
In the pediatric cancer alveolar rhabdomyosarcoma, the (2;13)(q35;q14) translocation juxtaposes PAX3 and FKHR to produce a chimeric PAX3-FKHR gene. With the use of Southern blot methodology, genomic rearrangements of PAX3 intron 7 were detected in 23 of 23 fusion-positive alveolar rhabdomyosarcomas and were not detected in 19 fusion-negative embryonal rhabdomyosarcomas. Rearrangements corresponding to the reciprocal FKHR-PAX3 fusion were detected in 21 of 23 PAX3-FKHR-positive cases, though FKHR-PAX3 transcripts were detected in only 15 of 23 cases. Mapping experiments demonstrated that breakpoints occurred throughout this 17.5 kb PAX3 intron and, in 12 of 23 cases, breakpoints clustered within a 4.5-kb region at the 3' end of the intron. Chromatin analysis revealed a prominent DNase I hypersensitive site at the 5' end of the intron but did not indicate any other DNA-protein interactions that might have affected the breakpoint distribution. Sequence analysis identified AT-rich regions within the 3' cluster, as well as alternating purine-pyrimidine and homopyrimidine elements at the borders of this cluster. These finding suggest that translocation breakpoints are constrained to PAX3 intron 7 primarily by functional boundaries related to the flanking exons and may be secondarily affected by sequence features within this intron.
在儿童癌症肺泡横纹肌肉瘤中，(2;13)(q35;q14)易位使PAX3和FKHR并列，产生嵌合的PAX3 - FKHR基因。使用Southern印迹法，在23例融合阳性的肺泡横纹肌肉瘤中检测到23例PAX3内含子7的基因组重排，而在19例融合阴性的胚胎性横纹肌肉瘤中未检测到。在23例PAX3 - FKHR阳性病例中的21例中检测到与相互的FKHR - PAX3融合相对应的重排，尽管在23例病例中仅在15例中检测到FKHR - PAX3转录本。定位实验表明，断点出现在整个17.5 kb的PAX3内含子中，并且在23例病例中的12例中，断点聚集在内含子3'端的一个4.5 kb区域内。染色质分析显示在内含子5'端有一个明显的DNase I超敏位点，但未表明可能影响断点分布的任何其他DNA - 蛋白质相互作用。序列分析确定了3'簇内富含AT的区域，以及该簇边界处交替的嘌呤 - 嘧啶和同嘧啶元件。这些发现表明，易位断点主要受与侧翼外显子相关的功能边界限制在PAX3内含子7中，并且可能其次受到该内含子内序列特征的影响。
