Dystrophin基因3～5号外显子缺失连接片段的克隆和测序

Cloning and sequencing of the junction fragment of dystrophin gene with exons 3 to 5 deletion

目的通过对抗肌萎缩蛋白(dystrophin)基因3-5号外显子缺失后连接片段的克隆和测序分析,探讨dystrophin基因缺失的发生机制。方法先以外显子PCR反应检测证实1例杜氏肌营养不良症患者3-5号外显子缺失,然后在2、5号内含子上用PCR步移方法寻找断裂位点,最后用靠近断裂位点处设计的引物,以PCR法直接扩增dystrophin基因的缺失连接片段并测序,测序结果和正常内含子序列作对比分析。结果获得2113bpPCR产物,本例基因缺失片段长约49000bp。5'端断裂点位于2号内含子短散在元件Alu序列内,3'端断裂点在单一序列,附近有TTTAAA序列。断裂点附近有较强的拓扑异构酶Ⅱ酶切位点。连接片段插入了26bp序列并在断裂点周围形成3个13bp的短序列重复(GGCTTATATTTAA)连接断裂点两端。结论推测重复序列、断裂点附近较强的拓扑异构酶Ⅱ酶切位点关联易引起基因的断裂重组,加上非同源末端连接修复机制等综合因素可能是导致基因缺失的重要原因。

Objective To study the mechanisms of dystrophin gene deletion by cloning and sequencing the junction fragment ofdystrophin gene with exons 3 to 5 deletion. Methods PCR was performed to verify dystrophin gene exons 3 to 5 deletion in a patient with Duchetme muscular dystrophy. A PCR-based genome-walking method was used to localize the breakpoint in introns 2 and 5, and the deletion-junction fragment was directly amplified by PCR approach with forward and reverse primers annealing to a DNA sequence as close as possible to the breakpoint in the introns 2 and 5. The sequencing result of the deletion-junction fragment was compared with the normal intron sequences. Results A sequence of 2113 bp containing the junction fragment was obtained. The 5＇ breakpoint was located in SINE/Alu element ofintron 2, and the 3＇ breakpoint was located in the unique sequence near the sequence TTTAAA. The breakpoints were associated with a strong topoisomerase Ⅱ cleavage site. A 26-bp fragment was inserted into the breakpoint and formed 3 duplications （GGCTTATATTTAA） of 13 bp around the deletion-junction fragment. Conclusion Repeat sequence and strong topoisomerase Ⅱ cleavage site around the breakpoint may predispose double-strand DNA breaks and recombination, which, in addition to the nonhomologous end-joining mechanism, may contribute as important factors to the gene deletion.