Salem Abdel-Halim, Ray David A, Hedges Dale J, Jurka Jerzy, Batzer Mark A
Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multi-scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana 70803, USA.
BMC Evol Biol. 2005 Feb 22;5:18. doi: 10.1186/1471-2148-5-18.
Alu elements are short (approximately 300 bp) interspersed elements that amplify in primate genomes through a process termed retroposition. The expansion of these elements has had a significant impact on the structure and function of primate genomes. Approximately 10 % of the mass of the human genome is comprised of Alu elements, making them the most abundant short interspersed element (SINE) in our genome. The majority of Alu amplification occurred early in primate evolution, and the current rate of Alu retroposition is at least 100 fold slower than the peak of amplification that occurred 30-50 million years ago. Alu elements are therefore a rich source of inter- and intra-species primate genomic variation.
A total of 153 Alu elements from the Ye subfamily were extracted from the draft sequence of the human genome. Analysis of these elements resulted in the discovery of two new Alu subfamilies, Ye4 and Ye6, complementing the previously described Ye5 subfamily. DNA sequence analysis of each of the Alu Ye subfamilies yielded average age estimates of approximately 14, approximately 13 and approximately 9.5 million years old for the Alu Ye4, Ye5 and Ye6 subfamilies, respectively. In addition, 120 Alu Ye4, Ye5 and Ye6 loci were screened using polymerase chain reaction (PCR) assays to determine their phylogenetic origin and levels of human genomic diversity.
The Alu Ye lineage appears to have started amplifying relatively early in primate evolution and continued propagating at a low level as many of its members are found in a variety of hominoid (humans, greater and lesser ape) genomes. Detailed sequence analysis of several Alu pre-integration sites indicated that multiple types of events had occurred, including gene conversions, near-parallel independent insertions of different Alu elements and Alu-mediated genomic deletions. A potential hotspot for Alu insertion in the Fer1L3 gene on chromosome 10 was also identified.
Alu元件是短（约300碱基对）散布元件，通过一种称为逆转座的过程在灵长类基因组中扩增。这些元件的扩张对灵长类基因组的结构和功能产生了重大影响。人类基因组约10%的质量由Alu元件组成，使其成为我们基因组中最丰富的短散布元件（SINE）。大多数Alu扩增发生在灵长类进化的早期，目前Alu逆转座的速率比3000万至5000万年前发生的扩增峰值至少慢100倍。因此，Alu元件是灵长类种间和种内基因组变异的丰富来源。
从人类基因组草图序列中提取了总共153个来自Ye亚家族的Alu元件。对这些元件的分析导致发现了两个新的Alu亚家族，Ye4和Ye6，补充了先前描述的Ye5亚家族。对每个Alu Ye亚家族的DNA序列分析得出，Alu Ye4、Ye5和Ye6亚家族的平均年龄估计分别约为1400万年、1300万年和约950万年。此外，使用聚合酶链反应（PCR）分析筛选了120个Alu Ye4、Ye5和Ye6位点，以确定它们的系统发育起源和人类基因组多样性水平。
Alu Ye谱系似乎在灵长类进化的相对早期就开始扩增，并以低水平持续传播，因为在各种类人猿（人类、大猩猩和小黑猩猩）基因组中发现了许多其成员。对几个Alu预整合位点的详细序列分析表明发生了多种类型的事件，包括基因转换、不同Alu元件的近平行独立插入以及Alu介导的基因组缺失。还在10号染色体上的Fer1L3基因中鉴定出一个Alu插入的潜在热点。
