Styles Pamela, Brookfield John F Y
Institute of Genetics, School of Biology, University of Nottingham, Queens Medical Centre, Nottingham, UK.
BMC Evol Biol. 2007 Jul 1;7:102. doi: 10.1186/1471-2148-7-102.
Alu elements are a family of SINE retrotransposons in primates. They are classified into subfamilies according to specific diagnostic mutations from the general Alu consensus. It is now believed that there may be several retrotranspositionally-competent source genes within an Alu subfamily. To investigate the evolution of young Alu elements it is critical to have access to complete subfamilies, which, following the release of the final human genome assembly, can now be obtained using in silico methods.
380 elements belonging to the young AluYg6 subfamily were identified in the human genome, a number significantly exceeding prior expectations. An AluYg6 element was also identified in the chimpanzee genome, indicating that the subfamily is older than previously estimated, and appears to have undergone a period of dormancy before its expansion. The relative contributions of back mutation and gene conversion to variation at the six diagnostic positions are examined, and cases of complete forward gene conversion events are reported. Two small subfamilies derived from AluYg6 have been identified, named AluYg6a2 and AluYg5b3, which contain 40 and 27 members, respectively. These small subfamilies are used to illustrate the ambiguity regarding Alu subfamily definition, and to assess the contribution of secondary source genes to the AluYg6 subfamily.
The number of elements in the AluYg6 subfamily greatly exceeds prior expectations, indicating that the current knowledge of young Alu subfamilies is incomplete, and that prior analyses that have been carried out using these data may have generated inaccurate results. A definition of primary and secondary source genes has been provided, and it has been shown that several source genes have contributed to the proliferation of the AluYg6 subfamily. Access to the sequence data for the complete AluYg6 subfamily will be invaluable in future computational analyses investigating the evolution of young Alu subfamilies.
Alu元件是灵长类动物中的一类短散在核元件（SINE）反转录转座子。它们根据与通用Alu共有序列的特定诊断性突变被分类为亚家族。现在人们认为，一个Alu亚家族中可能存在几个具有反转录转座能力的源基因。为了研究年轻Alu元件的进化，获取完整的亚家族至关重要，随着人类基因组最终组装版本的发布，现在可以通过计算机方法获得这些亚家族。
在人类基因组中鉴定出380个属于年轻AluYg6亚家族的元件，这一数量大大超过了先前的预期。在黑猩猩基因组中也鉴定出一个AluYg6元件，这表明该亚家族比先前估计的更古老，并且在其扩张之前似乎经历了一段休眠期。研究了六个诊断位置上回复突变和基因转换对变异的相对贡献，并报告了完全正向基因转换事件的案例。已鉴定出两个源自AluYg6的小亚家族，分别命名为AluYg6a2和AluYg5b3，它们分别包含40个和27个成员。这些小亚家族用于说明Alu亚家族定义的模糊性，并评估次要源基因对AluYg6亚家族的贡献。
AluYg6亚家族中的元件数量大大超过先前预期，表明目前对年轻Alu亚家族的了解并不完整，并且使用这些数据进行的先前分析可能产生了不准确的结果。提供了主要和次要源基因的定义，并表明几个源基因对AluYg6亚家族的增殖有贡献。获取完整AluYg6亚家族的序列数据在未来研究年轻Alu亚家族进化的计算分析中将非常宝贵。
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