Key Laboratory of Marine Bio-resource Sustainable Utilization (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, Republic of China.
BMC Genomics. 2013 Feb 15;14:103. doi: 10.1186/1471-2164-14-103.
Tandem repeats (TRs) in the mitochondrial (mt) genome control region have been documented in a wide variety of vertebrate species. The mechanism by which repeated tracts originate and undergo duplication and deletion, however, remains unclear.
We analyzed DNA sequences of mt genome TRs (mtTRs) in the ridged-eye flounder (Pleuronichthys cornutus), and characterized DNA sequences of mtTRs from other vertebrates using the data available in GenBank. Tandem repeats are concentrated in the control regions; however, we found approximately 16.6% of the TRs elsewhere in the mt genome. The flounder mtTRs possess three motif types with hypervariable characteristics at the 3' end of the control region (CR).
Based on our analysis of this larger dataset of mtTR sequences, we propose a novel model of Pause Melting Misalignment (PMM) to describe the birth and motif indel of tandem repeats. PMM is activated during a pause event in mitochondrial replication in which a dynamic competition between the nascent (N) heavy strand and the displaced (D) heavy strand may lead to the melting of the N-strand from the template (T) light strand. When mispairing occurs during rebinding of the N-strand, one or several motifs can be inserted or deleted in both strands during the next round of mt-replication or repair. This model can explain the characteristics of TRs in available vertebrate mt genomes.
串联重复（TRs）在线粒体（mt）基因组调控区已在多种脊椎动物物种中被记录。然而，重复片段起源并经历复制和缺失的机制仍不清楚。
我们分析了棱皮鱼（Pleuronichthys cornutus）mt 基因组 TRs（mtTRs）的 DNA 序列，并利用 GenBank 中可用的数据来描述其他脊椎动物的 mtTRs 的 DNA 序列。串联重复集中在调控区；然而，我们在 mt 基因组的其他地方发现了大约 16.6%的 TRs。该棱皮鱼 mtTRs 在调控区（CR）的 3'端具有三种具有高变异性特征的基序类型。
基于我们对更大的 mtTR 序列数据集的分析，我们提出了一个新的暂停熔化失配（PMM）模型来描述串联重复的产生和基序插入缺失。在线粒体复制过程中的暂停事件中激活 PMM，在该事件中，新生（N）重链和取代（D）重链之间的动态竞争可能导致 N 链从模板（T）轻链上熔化。当 N 链重新结合时发生错配时，在下一轮 mt 复制或修复过程中，两条链都可以插入或缺失一个或多个基序。该模型可以解释现有脊椎动物 mt 基因组中 TRs 的特征。
