Evolution-based screening enables genome-wide prioritization and discovery of DNA repair genes
Evolution-based screening enables genome-wide prioritization and discovery of DNA repair genes
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DOI：
10.1073/pnas.1906559116
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发表时间：
2019-09-24
影响因子：
11.1
通讯作者：
Bernstein, Kara A.
中科院分区：
文献类型：
--
作者：
Brunette, Gregory J.;Jamalruddin, Mohd A.;Bernstein, Kara A.
DNA修复是基因组稳定的关键，并通过保守途径维持。传统的全基因组哺乳动物筛查既昂贵又费力。然而，计算方法规避了这些限制，是识别新的DNA修复因子的有力工具。通过分析主要DNA修复途径中基因之间的进化关系，我们揭示了单个基因与鉴定的伙伴之间的功能关系。在这里，我们将17487个哺乳动物基因与6种不同的DNA修复途径进行了共同进化排序。与同源重组或范可尼贫血因子的基因筛选直接比较表明，我们的基于进化的筛选与传统的筛选方法相比，即使不是更好，也是相当的。基于DNA损伤诱导凋亡抑制基因（DDIAS）与同源重组的共同进化，我们确定了DDIAS基因在双链断裂修复中的作用，证明了我们的策略的实用性。DDIAS敲低导致DNA双链断裂，通过ATM激酶激活和53BP1病灶诱导表明。此外，ddias缺失的细胞缺乏同源重组。我们的研究结果表明，进化分析是发现DNA修复中的新因素和功能关系的有力工具。
DNA repair is critical for genome stability and is maintained through conserved pathways. Traditional genome-wide mammalian screens are both expensive and laborious. However, computational approaches circumvent these limitations and are a powerful tool to identify new DNA repair factors. By analyzing the evolutionary relationships between genes in the major DNA repair pathways, we uncovered functional relationships between individual genes and identified partners. Here we ranked 17,487 mammalian genes for coevolution with 6 distinct DNA repair pathways. Direct comparison to genetic screens for homologous recombination or Fanconi anemia factors indicates that our evolution-based screen is comparable, if not superior, to traditional screening approaches. Demonstrating the utility of our strategy, we identify a role for the DNA damage-induced apoptosis suppressor (DDIAS) gene in double-strand break repair based on its coevolution with homologous recombination. DDIAS knockdown results in DNA double-strand breaks, indicated by ATM kinase activation and 53BP1 foci induction. Additionally, DDIAS-depleted cells are deficient for homologous recombination. Our results reveal that evolutionary analysis is a powerful tool to uncover novel factors and functional relationships in DNA repair.