Numt-mediated double-strand break repair mitigates deletions during primate genome evolution.
Numt-mediated double-strand break repair mitigates deletions during primate genome evolution.
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DOI：
10.1371/journal.pgen.1000237
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发表时间：
2008-10
期刊：
影响因子：
4.5
通讯作者：
Covo S
中科院分区：
文献类型：
--
作者：
Hazkani-Covo E;Covo S
非同源末端连接（NHEJ）是哺乳动物细胞双链断裂修复（DSBR）的主要机制。NHEJ传统上是从涉及诱导双链断裂（DSB）的实验系统中推断出来的。在实验NHEJ中观察到的修复事件谱是否反映了在染色体进化过程中NHEJ对自然断裂的修复是一个尚未解决的问题。在灵长类动物的染色体发生中，线粒体起源的核DNA序列numts通过NHEJ插入到天然存在的染色体断裂中。因此，numt整合位点为在进化时间尺度上作用于基因组的机制提供了证据。我们已经确定了35和55个谱系特异性numt在人类和黑猩猩基因组，分别使用恒河猴基因组作为外群。根据修复模式对152个染色体融合点进行了分类。修复涉及微同源性和修复导致核苷酸添加被检测到。这些修复模式在经典NHEJ的实验确定范围内，这表明来自实验系统的信息代表了更广泛的遗传基因座和末端配置。然而，在不相容的DSBR事件中，总是发生小的缺失，而在54%的numt整合事件中，没有检测到缺失。即使与涉及填充物DNA的DSBR相比，Numts也显示缺失频率的统计学显著降低。因此，numts通过NHEJ显示出独特的整合机制。由于numt插入过程中的缺失频率较低，染色体断裂的天然突出端得以保留，这使我们能够确定24%的分析断裂与多达11个碱基的突出端具有粘性。据我们所知，这些数据代表了对天然存在的DSB结构的最全面的描述。我们提出了一个模型，其中密封的DSB的numts，并可能由其他填料DNA，防止核处理的DSB，可能会导致有害的修复。DNA序列的变化是进化中变异的主要来源。这些变化通常是由DNA损伤引起的，这种损伤以一种无法恢复原始序列的方式修复。一种类型的DNA损伤是染色体双链断裂。这种断裂主要是在模型系统中进行实验研究，因为自然发生的染色体断裂很难跟踪。在这里，我们使用进化的方法来研究自然发生的染色体断裂的修复。在整个进化史中，线粒体基因组的片段，称为numts（线粒体起源的核序列），被插入到核基因组中。numt被被动捕获到随机的染色体断裂中，在基因组中留下序列痕迹。人类和黑猩猩有一个共同的祖先，他们的基因组具有很高的序列相似性，因此，他们的物种特异性numts可以用来跟踪一些断裂结构和修复机制。将自然发生的断裂和修复模式与实验修复模式进行比较，发现了相似之处，但也突出了明显的差异。实验性断裂通常涉及缺失，而在基于numt的修复系统中缺失的频率明显较低。我们认为，染色体外DNA序列，如numts，在保持基因组的完整性，保护自然发生的染色体断裂进一步有害的处理中发挥作用。
Non-homologous end joining (NHEJ) is the major mechanism of double-strand break repair (DSBR) in mammalian cells. NHEJ has traditionally been inferred from experimental systems involving induced double strand breaks (DSBs). Whether or not the spectrum of repair events observed in experimental NHEJ reflects the repair of natural breaks by NHEJ during chromosomal evolution is an unresolved issue. In primate phylogeny, nuclear DNA sequences of mitochondrial origin, numts, are inserted into naturally occurring chromosomal breaks via NHEJ. Thus, numt integration sites harbor evidence for the mechanisms that act on the genome over evolutionary timescales. We have identified 35 and 55 lineage-specific numts in the human and chimpanzee genomes, respectively, using the rhesus monkey genome as an outgroup. One hundred and fifty two numt-chromosome fusion points were classified based on their repair patterns. Repair involving microhomology and repair leading to nucleotide additions were detected. These repair patterns are within the experimentally determined spectrum of classical NHEJ, suggesting that information from experimental systems is representative of broader genetic loci and end configurations. However, in incompatible DSBR events, small deletions always occur, whereas in 54% of numt integration events examined, no deletions were detected. Numts show a statistically significant reduction in deletion frequency, even in comparison to DSBR involving filler DNA. Therefore, numts show a unique mechanism of integration via NHEJ. Since the deletion frequency during numt insertion is low, native overhangs of chromosome breaks are preserved, allowing us to determine that 24% of the analyzed breaks are cohesive with overhangs of up to 11 bases. These data represent, to the best of our knowledge, the most comprehensive description of the structure of naturally occurring DSBs. We suggest a model in which the sealing of DSBs by numts, and probably by other filler DNA, prevents nuclear processing of DSBs that could result in deleterious repair. Changes to DNA sequence are the major source of variation in evolution. Those changes often arise from damage to DNA that is repaired in a way that fails to restore the original sequence. One type of DNA damage is a chromosomal double-strand break. Such breaks are mostly studied experimentally in model systems, because naturally occurring chromosomal breaks are hard to follow. Here, we used an evolutionary approach to study the repair of naturally occurring chromosomal breaks. Throughout evolutionary history, fragments of the mitochondrial genome, known as numts (nuclear sequences of mitochondrial origin), have been inserted into the nuclear genome. Numts are passively captured into random chromosomal breaks, leaving sequence traces in genomes. Humans and chimpanzees share a recent common ancestor and their genomes share high sequence similarity; therefore, their species-specific numts can be used to follow both some of the break structure and repair mechanisms. Comparing naturally occurring break and repair patterns with experimental repair patterns identified similarities but also highlighted a clear difference. Experimental breaks usually involve deletions, while deletions were significantly less frequent in the numt based repair system. We propose that extra-chromosomal DNA sequences, like numts, play a role in maintaining genome integrity by protecting naturally occurring chromosomal breaks from further deleterious processing.
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DNA聚合酶MU参与哺乳动物细胞中DNA双链断裂的特定子集的修复。
影响因子：
14.9
作者：
Capp, Jean-Pascal;Boudsocq, Francois;Besnard, Anne-Gaelle;Lopez, Bernard S;Cazaux, Christophe;Hoffmann, Jean-Sebastien;Canitrot, Yvan
通讯作者：
Canitrot, Yvan
影响因子：
3.9
作者：
Goldin, E;Stahl, S;Schiffmann, R
通讯作者：
Schiffmann, R
DOI：
10.1073/pnas.042694899
发表时间：
2002-07-23
影响因子：
11.1
作者：
Adams, KL;Qiu, YL;Palmer, JD
通讯作者：
Palmer, JD
影响因子：
4.5
作者：
Han, Kyudong;Lee, Jungnam;Batzer, Mark A.
通讯作者：
Batzer, Mark A.
影响因子：
64.8
作者：
Cheng, Z;Ventura, M;Eichler, EE
通讯作者：
Eichler, EE