Sheen F M, Sherry S T, Risch G M, Robichaux M, Nasidze I, Stoneking M, Batzer M A, Swergold G D
Promega Corporation, Madison, Wisconsin 53711, USA.
Genome Res. 2000 Oct;10(10):1496-508. doi: 10.1101/gr.149400.
The insertion of mobile elements into the genome represents a new class of genetic markers for the study of human evolution. Long interspersed elements (LINEs) have amplified to a copy number of about 100,000 over the last 100 million years of mammalian evolution and comprise approximately 15% of the human genome. The majority of LINE-1 (L1) elements within the human genome are 5' truncated copies of a few active L1 elements that are capable of retrotransposition. Some of the young L1 elements have inserted into the human genome so recently that populations are polymorphic for the presence of an L1 element at a particular chromosomal location. L1 insertion polymorphisms offer several advantages over other types of polymorphisms for human evolution studies. First, they are typed by rapid, simple, polymerase chain reaction (PCR)-based assays. Second, they are stable polymorphisms that rarely undergo deletion. Third, the presence of an L1 element represents identity by descent, because the probability is negligible that two different young L1 repeats would integrate independently between the exact same two nucleotides. Fourth, the ancestral state of L1 insertion polymorphisms is known to be the absence of the L1 element, which can be used to root plots/trees of population relationships. Here we report the development of a PCR-based display for the direct identification of dimorphic L1 elements from the human genome. We have also developed PCR-based assays for the characterization of six polymorphic L1 elements within the human genome. PCR analysis of human/rodent hybrid cell line DNA samples showed that the polymorphic L1 elements were located on several different chromosomes. Phylogenetic analysis of nonhuman primate DNA samples showed that all of the recently integrated "young" L1 elements were restricted to the human genome and absent from the genomes of nonhuman primates. Analysis of a diverse array of human populations showed that the allele frequencies and level of heterozygosity for each of the L1 elements was variable. Polymorphic L1 elements represent a new source of identical-by-descent variation for the study of human evolution. [The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF242435-AF242451.]
可移动元件插入基因组代表了一类用于人类进化研究的新型遗传标记。在过去一亿年的哺乳动物进化过程中，长散在重复序列（LINEs）已扩增至约100,000个拷贝数，约占人类基因组的15%。人类基因组中的大多数LINE-1（L1）元件是少数能够逆转录转座的活跃L1元件的5'端截短拷贝。一些年轻的L1元件最近才插入人类基因组，以至于在特定染色体位置上L1元件的存在在人群中呈多态性。与其他类型的多态性相比，L1插入多态性在人类进化研究中具有几个优势。首先，它们通过基于聚合酶链反应（PCR）的快速、简单检测方法进行分型。其次，它们是稳定的多态性，很少发生缺失。第三，L1元件的存在代表同源性，因为两个不同的年轻L1重复序列在完全相同的两个核苷酸之间独立整合的概率可以忽略不计。第四，已知L1插入多态性的祖先状态是不存在L1元件，这可用于构建群体关系图/树的根。在此，我们报告了一种基于PCR的展示方法的开发，用于直接从人类基因组中鉴定二态性L1元件。我们还开发了基于PCR的检测方法来表征人类基因组中的六个多态性L1元件。对人/啮齿动物杂交细胞系DNA样本的PCR分析表明，多态性L1元件位于几条不同的染色体上。对非人类灵长类动物DNA样本的系统发育分析表明，所有最近整合的“年轻”L1元件都局限于人类基因组，在非人类灵长类动物基因组中不存在。对各种人类群体的分析表明，每个L1元件的等位基因频率和杂合度水平是可变的。多态性L1元件代表了用于人类进化研究的同源变异的新来源。[本文所述的序列数据已提交至GenBank数据库，登录号为AF242435 - AF242451。]
