Band-array detection of chromosomal rearrangements in diploid yeast cells exposed to ionizing radiation

At the organismal level, genome rearrangements are usually deleterious and are often associated with disease. Yet, on an evolutionary scale, they can be beneficial as they provide for rapid genetic diversification. DNA lesions, particularly double-strand breaks (DSBs), are sources of genome instability that can be rectified by various repair processes. Homologous recombination (HR) is highly effective at protecting the genome from DSBs and provides for accurate repair between sister chromatids and homologous chromosomes. Here we show that although random DSBs induced by ionizing radiation in yeast chromosomes are repaired efficiently by HR in G-2 diploid cells, rearrangements are frequent. The chromosome aberrations (ABs) primarily resulted from recombination between Ty retrotransposable elements, the most abundant class of dispersed repetitive DNAs in the genome, while some rearrangements involved other classes of repetitive DNA. Few, if any, of the ABs could be attributed to nonhomologous end-joining (NHEJ). We conclude that only those few DSBs that fall at or near the 3-5% of the genome composed of repetitive DNA elements are effective at generating rearrangements, while other lesions that appear in unique (single copy) sequences are correctly repaired. Thus, by successfully competing with repair that normally occurs between large homologous chromosomal DNAs, the combination of repetitive elements and DSBs provides genome plasticity and a rich source of evolutionary opportunities. Keywords: Band-array Each array in this series corresponds to the DNA of a yeast chromosomal band excised from a pulse-field gel (CHEF). Chromosomal aberrations identified in radiation survivors were analyzed by microarray to reveal which regions of the genome were present in the new chromosomes. The DNA enriched in the specific band appears in the arrays as continuos segments of spots with highly positive Log2 Red/Green ratios.

在生物体层面，基因组重排通常具有有害性，且常与疾病相关。然而从进化尺度来看，它们可带来益处，因为能促成快速的遗传多样化。DNA损伤，尤其是双链断裂（double-strand breaks，DSBs），是基因组不稳定的诱因，可通过多种修复过程得以纠正。同源重组（homologous recombination，HR）在保护基因组免受DSBs损伤方面效果显著，且能实现姐妹染色单体与同源染色体间的精准修复。
本研究表明，尽管酵母染色体中由电离辐射诱导的随机DSBs可在G2期二倍体细胞中通过HR被高效修复，但重排事件却频繁发生。此类染色体畸变（chromosome aberrations，ABs）主要源于Ty反转录转座因子之间的重组——这类因子是基因组中丰度最高的散在重复DNA类群，部分重排则涉及其他类型的重复DNA。几乎无（若有的话）染色体畸变可归因于非同源末端连接（nonhomologous end-joining，NHEJ）。
我们得出结论：仅那些发生在占基因组3%-5%的重复DNA元件内部或其附近的少量DSBs，才会有效引发基因组重排；而出现在单拷贝序列中的其他损伤则会被正确修复。因此，通过与通常发生在大型同源染色体DNA间的修复过程成功竞争，重复元件与DSBs的共同作用赋予了基因组可塑性，并为进化提供了丰富的机遇。
关键词：条带微阵列（Band-array）
本系列中的每一张微阵列，均对应从脉冲场凝胶（CHEF）中切取的酵母染色体条带的DNA。研究人员通过微阵列分析了辐射存活者中鉴定出的染色体畸变，以揭示新染色体中包含哪些基因组区域。富集于特定条带的DNA，会以具有高度正值Log2红绿比值的连续斑点区段形式出现在微阵列中。