A comprehensive analysis of recently integrated human Ta L1 elements
A comprehensive analysis of recently integrated human Ta L1 elements
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DOI：
10.1086/341718
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发表时间：
2002-08-01
影响因子：
9.8
通讯作者：
Batzer, MA
中科院分区：
文献类型：
--
作者：
Myers, JS;Vincent, BJ;Batzer, MA
L1 LINEs的Ta（（t）在bar下，bar下的子集（a）在bar下）亚家族（（l）在bar下，（i）在bar下，（e）在bar下）的特征在于在3个非翻译区中的3-bp ACA序列，并且在人类基因组中包含类似于520个成员。在此，我们从人类基因组序列草案中提取了468个Ta L1 H（（L1）在bar（h）下在bar（s）下在bar specific）元件，并使用聚合酶链反应（PCR）测定筛选单个元件，以确定它们的系统发育起源和人类基因组多样性水平。124个适合于完整序列分析的元件是全长的（类似于6 kb），并且显然没有任何5'端截短。这些全长元件中有44个具有两个完整的开放阅读框架，并且可能能够反转录。Ta L1元件的序列分析显示核苷酸分歧水平较低，估计年龄为199万年，表明L1 Ta亚家族的扩张发生在人类和非洲猿的分歧之后。共262钽L1元素进行了筛选与PCR为基础的测定，以确定其系统发育起源和人类基因组变异水平与每个元素。通过PCR分析的所有Ta L1元件均不存在于非人灵长类动物基因组中的邻位位置，除了一个单一元件（L1 HS 72）也存在于普通黑猩猩（Pan troglodytes）和侏儒黑猩猩（P. paniscus）基因组中。序列分析表明，这个单一的例外是一个基因转换事件的产物，涉及一个较老的预先存在的L1元件。一百一十五（45%）的Ta L1元件是多态性的插入存在或不存在，并将作为人类进化研究的血统相同的标记。
The Ta ((t) under bar ranscribed, subset (a) under bar) subfamily of L1 LINEs ((l) under bar ong (i) under bar nterspersed (e) under bar lements) is characterized by a 3-bp ACA sequence in the 3 untranslated region and contains similar to520 members in the human genome. Here, we have extracted 468 Ta L1Hs ((L1) under bar (h) under bar uman (s) under bar pecific) elements from the draft human genomic sequence and screened individual elements using polymerase-chain-reaction (PCR) assays to determine their phylogenetic origin and levels of human genomic diversity. One hundred twenty-four of the elements amenable to complete sequence analysis were full length (similar to6 kb) and have apparently escaped any 5' truncation. Forty-four of these full-length elements have two intact open reading frames and may be capable of retrotransposition. Sequence analysis of the Ta L1 elements showed a low level of nucleotide divergence with an estimated age of 1.99 million years, suggesting that expansion of the L1 Ta subfamily occurred after the divergence of humans and African apes. A total of 262 Ta L1 elements were screened with PCR-based assays to determine their phylogenetic origin and the level of human genomic variation associated with each element. All of the Ta L1 elements analyzed by PCR were absent from the orthologous positions in nonhuman primate genomes, except for a single element (L1HS72) that was also present in the common (Pan troglodytes) and pygmy (P. paniscus) chimpanzee genomes. Sequence analysis revealed that this single exception is the product of a gene conversion event involving an older preexisting L1 element. One hundred fifteen (45%) of the Ta L1 elements were polymorphic with respect to insertion presence or absence and will serve as identical-by-descent markers for the study of human evolution.