MAMMALIAN TRANSPOSONS

哺乳动物L1元素（LINE-1）通过将其RNA转录本复制到DNA中，然后将DNA整合到基因组中进行复制。在过去的1500万年里，这一过程在小鼠基因组中产生了约55万kb的L1 DNA，约占总数的20%。在人类中，L1逆转录导致了0.2%的遗传缺陷。~7 kb的L1元素有四个区域：一个5未翻译区域（UTR）；两个开放阅读框架（orf I和orf II）；一个3utr。5 UTR具有调控功能，ORF I蛋白结合RNA， ORF II蛋白是逆转录酶和核酸内切酶，3 UTR形成复杂的链内DNA和RNA结构。我们和其他人已经确定了啮齿动物L1元素的进化动力学，并表明它们随着新家族不断取代旧家族而迅速进化。由于过去L1家族的产物被保留，现代基因组包含过去和现在复制成功的L1亚家族。L1 DNA的亚家族结构允许对L1基因组的功能分析和L1元件的自然历史进行比较。了解L1元素的自然历史对于解决一些问题是必要的，例如新的L1家族是如何产生的，以及L1元素对其宿主的影响。因此，我们一直在研究灵长类动物（包括人类）L1元素的进化动力学，令人惊讶的是，这还没有被研究过。我们把重点放在所谓的Ta家族上，因为迄今为止确定的两个推定活跃的人类L1基因都是这个家族的成员。结果表明：Ta家族至少由Ta-0和Ta-1两个亚家族组成。Ta-0家族大约在500万年前（Mya）出现，并在1-2亿年前达到扩增高峰。虽然Ta-1亚家族仍然保留了一些活性，但Ta-1在大约3亿年前出现，似乎正在取代Ta-0获得复制优势。与这些亚家族的相对年龄一致，全球人群中47%的Ta-0插入片段是固定的（17个位点中的8个），但只有23%的Ta-1插入片段是固定的（30个位点中的7个）。Ta家族仅存在于人类中，现在每个单倍体基因组包含约700个成员，其中300个属于Ta-1亚家族。Ta-1元素每代的积累速度与最近进化的啮齿动物L1家族相同。尽管Ta-1亚家族具有突出的地位和近期的活性，但在先前旨在鉴定全长人类L1元件的研究中却遗漏了Ta-1亚家族。因此，先前的结果严重低估了潜在活性人类L1元件的数量及其遗传影响。系统发育分析揭示的Ta-1亚家族再次证明了这种研究L1生物学的方法是正确的。鉴于遗传多态性对遗传作图和群体遗传学的重要性，我们开发了一种方法来分离和表征几个人群中所有L1相关多态性。我们还希望利用这些结果开发L1转位率（而不是积累率）的测定方法。我们刚刚完成这项工作的第一阶段，即隔离Ta-1家族的每一个成员。此外，为在其他人群中分离多态性位点提供基础工作，了解整个L1家族的遗传环境可能有助于确定导致其繁殖成功的因素。最后，我们还分析了其他人科动物L1的进化动态，并对来自黑猩猩、大猩猩和猩猩的大量L1元素进行了约600 bp的测序。此外，我们正在比较这些动物和人类L1插入同源位点之间的序列差异，以获得一个可靠的原始人分子钟值。这一价值不仅对我们的研究有用，而且对其他物种的比较基因组学研究也有帮助。-反转录转座子遗传多态性进化L1基因组学哺乳动物灵长类动物DNA系统发育

Mammalian L1 elements (LINE-1) replicate by copying their RNA transcripts into DNA which is then integrated into the genome. In the last 15 million years this process has generated ~550,000 kb of L1 DNA in murine genomes, ~ 20% of the total. In humans L1 retrotransposition causes up to 0.2% of the genetic defects. The ~7 kb L1 element has four regions: a 5 untranslated region, (UTR); two open reading frames (ORFs I and II); a 3 UTR. The 5 UTR has a regulatory function, the ORF I protein binds RNA, the ORF II protein is a reverse transcriptase and endonuclease, and the 3 UTR forms complex intrastrand DNA and RNA structures. We, and others, have determined the evolutionary dynamics of rodent L1 elements and showed that they evolve rapidly with novel families continually replacing older ones. Since the products of past L1 families are retained, modern genomes contain both past and present replicatively successful L1 subfamilies. The subfamily structure of L1 DNA permits a comparative approach to the functional analysis of the L1 genome and for determining the natural history of L1 elements. Understanding the natural history of L1 elements is necessary for addressing several issues such as how novel L1 families arise, and the impact of L1 elements on their hosts. Accordingly, we have been examining the evolutionary dynamics of L1 elements in primates, including humans, which surprisingly had not yet been examined. We focused on the so called Ta family since the two putatively active human L1 elements so far identified are members of this family. We made the following findings: The Ta family consists of at least two subfamilies, Ta-0 and Ta-1. The Ta-0 family arose about 5 million years ago (Mya) and reached peak amplification 1-2 Mya. Ta-1 appeared ~3 Mya and it is seemingly replacing Ta-0 for replicative supremacy, although the Ta-0 subfamily still retains some activity. In agreement with the relative ages of these subfamilies, 47% of Ta-0 inserts are fixed in world wide human populations (8 of 17 loci), but only 23% (7 of 30 loci) of Ta-1 inserts are fixed. The Ta family is present only in humans and now contains about 700 members per haploid genome, 300 of which belong to the Ta-1 subfamily. Ta-1 elements have been accumulating at the same rate per generation as recently evolved rodent L1 families. Despite its prominence and recent activity, the Ta-1 subfamily was missed in a previous study aimed at identifying full length human L1 elements. Therefore, the previous results seriously under estimated both the number of potentially active human L1 elements and their genetic impact. The revelation of the Ta-1 subfamily by our phylogenetic analysis again vindicates this approach for investigating L1 biology. Given the importance of genetic polymorphisms for genetic mapping and population genetics we developed a method to isolate and characterize all of the L1 related polymorphisms in several human populations. We also hope to use these results to develop an assay for the L1 transposition rate (as opposed to the accumulation rate). We have just about completed the first phase of this work, namely the isolation of every member of the Ta-1 family. In addition, to providing the ground work for isolating polymorphic loci in other human populations, knowing the genetic environment of an entire L1 family may prove useful in identifying those factors responsible for its replicative success. And finally, we are also analyzing the evolutionary dynamics of L1 in other hominids, and have sequenced ~600 bp of a large number of L1 elements from chimpanzee, gorilla, and orangutan. In addition we are comparing sequence divergence between homologous sites of L1 insertion in these animals and humans in order to obtain a robust value the for the hominid molecular clock. This value will be not only useful for our studies but also to others on the comparative genomics of these species. - retrotransposons genetics polymorphism evolution L1 genomics mammals primates DNA phylogenetics