Putnam Christopher D, Pallis Katielee, Hayes Tikvah K, Kolodner Richard D
Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, La Jolla, California, United States of America; Department of Medicine, University of California School of Medicine, San Diego, La Jolla, California, United States of America.
Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, La Jolla, California, United States of America.
PLoS Genet. 2014 Apr 3;10(4):e1004277. doi: 10.1371/journal.pgen.1004277. eCollection 2014 Apr.
Whole genome sequencing of cancer genomes has revealed a diversity of recurrent gross chromosomal rearrangements (GCRs) that are likely signatures of specific defects in DNA damage response pathways. However, inferring the underlying defects has been difficult due to insufficient information relating defects in DNA metabolism to GCR signatures. By analyzing over 95 mutant strains of Saccharomyces cerevisiae, we found that the frequency of GCRs that deleted an internal CAN1/URA3 cassette on chrV L while retaining a chrV L telomeric hph marker was significantly higher in tel1Δ, sae2Δ, rad53Δ sml1Δ, and mrc1Δ tof1Δ mutants. The hph-retaining GCRs isolated from tel1Δ mutants contained either an interstitial deletion dependent on non-homologous end-joining or an inverted duplication that appeared to be initiated from a double strand break (DSB) on chrV L followed by hairpin formation, copying of chrV L from the DSB toward the centromere, and homologous recombination to capture the hph-containing end of chrV L. In contrast, hph-containing GCRs from other mutants were primarily interstitial deletions (mrc1Δ tof1Δ) or inverted duplications (sae2Δ and rad53Δ sml1Δ). Mutants with impaired de novo telomere addition had increased frequencies of hph-containing GCRs, whereas mutants with increased de novo telomere addition had decreased frequencies of hph-containing GCRs. Both types of hph-retaining GCRs occurred in wild-type strains, suggesting that the increased frequencies of hph retention were due to the relative efficiencies of competing DNA repair pathways. Interestingly, the inverted duplications observed here resemble common GCRs in metastatic pancreatic cancer.
癌症基因组的全基因组测序揭示了多种常见的染色体大片段重排（GCRs），这些重排可能是DNA损伤反应途径中特定缺陷的标志。然而，由于将DNA代谢缺陷与GCR特征相关联的信息不足，推断潜在缺陷一直很困难。通过分析95株以上的酿酒酵母突变株，我们发现，在tel1Δ、sae2Δ、rad53Δ sml1Δ和mrc1Δ tof1Δ突变体中，删除V L染色体上内部CAN1/URA3盒同时保留V L染色体端粒hph标记的GCR频率显著更高。从tel1Δ突变体中分离出的保留hph的GCRs包含一个依赖于非同源末端连接的间隙缺失或一个反向重复，该反向重复似乎由V L染色体上的双链断裂（DSB）引发，随后形成发夹结构，从DSB向着丝粒复制V L染色体，并通过同源重组捕获V L染色体含hph的末端。相比之下，来自其他突变体的含hph的GCRs主要是间隙缺失（mrc1Δ tof1Δ）或反向重复（sae2Δ和rad53Δ sml1Δ）。端粒从头添加受损的突变体中含hph的GCR频率增加，而端粒从头添加增加的突变体中含hph的GCR频率降低。两种类型的保留hph的GCRs都出现在野生型菌株中，这表明hph保留频率的增加是由于竞争性DNA修复途径的相对效率。有趣的是，这里观察到的反向重复类似于转移性胰腺癌中常见的GCRs。
