Navrátilová Alice, Koblízková Andrea, Macas Jirí
Biology Centre ASCR, Institute of Plant Molecular Biology, Branisovská 31, Ceské Budejovice, CZ-37005, Czech Republic.
BMC Plant Biol. 2008 Aug 22;8:90. doi: 10.1186/1471-2229-8-90.
Satellite repeats represent one of the most dynamic components of higher plant genomes, undergoing rapid evolutionary changes of their nucleotide sequences and abundance in a genome. However, the exact molecular mechanisms driving these changes and their eventual regulation are mostly unknown. It has been proposed that amplification and homogenization of satellite DNA could be facilitated by extrachromosomal circular DNA (eccDNA) molecules originated by recombination-based excision from satellite repeat arrays. While the models including eccDNA are attractive for their potential to explain rapid turnover of satellite DNA, the existence of satellite repeat-derived eccDNA has not yet been systematically studied in a wider range of plant genomes.
We performed a survey of eccDNA corresponding to nine different families and three subfamilies of satellite repeats in ten species from various genera of higher plants (Arabidopsis, Oryza, Pisum, Secale, Triticum and Vicia). The repeats selected for this study differed in their monomer length, abundance, and chromosomal localization in individual species. Using two-dimensional agarose gel electrophoresis followed by Southern blotting, eccDNA molecules corresponding to all examined satellites were detected. EccDNA occurred in the form of nicked circles ranging from hundreds to over eight thousand nucleotides in size. Within this range the circular molecules occurred preferentially in discrete size intervals corresponding to multiples of monomer or higher-order repeat lengths.
This work demonstrated that satellite repeat-derived eccDNA is common in plant genomes and thus it can be seriously considered as a potential intermediate in processes driving satellite repeat evolution. The observed size distribution of circular molecules suggests that they are most likely generated by molecular mechanisms based on homologous recombination requiring long stretches of sequence similarity.
卫星重复序列是高等植物基因组中最具动态性的组成部分之一，其核苷酸序列和基因组丰度经历快速的进化变化。然而，驱动这些变化的确切分子机制及其最终调控大多未知。有人提出，卫星DNA的扩增和同质化可能由基于重组的从卫星重复序列阵列中切除产生的染色体外环状DNA（eccDNA）分子所促进。虽然包括eccDNA在内的模型因其解释卫星DNA快速周转的潜力而具有吸引力，但卫星重复序列衍生的eccDNA的存在尚未在更广泛的植物基因组中进行系统研究。
我们对来自高等植物不同属（拟南芥、水稻、豌豆、黑麦、小麦和蚕豆）的10个物种中对应于9个不同家族和3个卫星重复序列亚家族的eccDNA进行了调查。本研究选择的重复序列在单个物种中的单体长度、丰度和染色体定位方面存在差异。使用二维琼脂糖凝胶电泳，随后进行Southern印迹，检测到了对应于所有检测卫星的eccDNA分子。EccDNA以切口环状形式出现，大小从数百到八千多个核苷酸不等。在此范围内，环状分子优先出现在对应于单体或高阶重复长度倍数的离散大小区间内。
这项工作表明，卫星重复序列衍生的eccDNA在植物基因组中很常见，因此可以被认真视为驱动卫星重复序列进化过程中的潜在中间体。观察到的环状分子大小分布表明，它们很可能是由基于需要长序列相似性的同源重组的分子机制产生的。
