Lujan Scott A, Clark Alan B, Kunkel Thomas A
Genome Instability and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.
Genome Instability and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
Nucleic Acids Res. 2015 Apr 30;43(8):4067-74. doi: 10.1093/nar/gkv271. Epub 2015 Mar 30.
Mutation rates are used to calibrate molecular clocks and to link genetic variants with human disease. However, mutation rates are not uniform across each eukaryotic genome. Rates for insertion/deletion (indel) mutations have been found to vary widely when examined in vitro and at specific loci in vivo. Here, we report the genome-wide rates of formation and repair of indels made during replication of yeast nuclear DNA. Using over 6000 indels accumulated in four mismatch repair (MMR) defective strains, and statistical corrections for false negatives, we find that indel rates increase by 100 000-fold with increasing homonucleotide run length, representing the greatest effect on replication fidelity of any known genomic parameter. Nonetheless, long genomic homopolymer runs are overrepresented relative to random chance, implying positive selection. Proofreading defects in the replicative polymerases selectively increase indel rates in short repetitive tracts, likely reflecting the distance over which Pols δ and ϵ interact with duplex DNA upstream of the polymerase active site. In contrast, MMR defects hugely increase indel mutagenesis in long repetitive sequences. Because repetitive sequences are not uniformly distributed among genomic functional elements, the quantitatively different consequences on genome-wide repeat sequence instability conferred by defects in proofreading and MMR have important biological implications.
突变率被用于校准分子钟，并将基因变异与人类疾病联系起来。然而，每个真核生物基因组中的突变率并不均匀。在体外研究以及体内特定基因座处检测时，插入/缺失（indel）突变的发生率差异很大。在此，我们报告了酵母核DNA复制过程中indel形成和修复的全基因组发生率。利用在四个错配修复（MMR）缺陷菌株中积累的6000多个indel，并对假阴性进行统计校正，我们发现随着同核苷酸连续长度增加，indel发生率增加10万倍，这代表了任何已知基因组参数对复制保真度的最大影响。尽管如此，相对于随机概率，长基因组同聚物连续片段的占比过高，这意味着存在正选择。复制性聚合酶中的校对缺陷在短重复序列中选择性地增加indel发生率，这可能反映了聚合酶δ和ε与聚合酶活性位点上游双链DNA相互作用的距离。相比之下，MMR缺陷在长重复序列中极大地增加了indel诱变。由于重复序列并非均匀分布于基因组功能元件之间，校对和MMR缺陷对全基因组重复序列不稳定性造成的数量上不同的后果具有重要的生物学意义。
