Mammalian Transposons

哺乳动物L1元素（LINE-1）通过将其RNA转录物复制到DNA中进行复制（逆转录），然后将DNA整合到基因组中。早在哺乳动物受辐射100亿年前，L1元件就开始在哺乳动物基因组中复制和进化。L1元素占人类基因组的17%，并导致高达0.2%的遗传缺陷。此外，它们可能催化高度重复的SINE （Alu）家族和加工过的假基因的逆转录。大约6 kb的人类L1元素有四个区域：A 5？UTR（非翻译区）具有调节功能；ORF I编码RNA结合蛋白；ORF II编码L1 cDNA复制酶；3吗?UTR包含一个保守的富g多嘌呤基序。我们发现啮齿类动物和人类的L1元素都在快速进化，新的家族不断取代旧的家族。由于过去L1家族的大部分拷贝被保留，现代基因组包含祖先和现代L1家族。已经灭绝的L1科的遗迹可以提供宿主物种的系统发育信息和重要的遗传参数，如中性突变率。由当前复制家族产生的L1插入为分析群体结构提供了强大的多态性遗传标记。我们继续对人类tal1家族进行分析，重点是分离我们最近发现的产生Ta1亚家族的插入。由于这个家族目前在人类中扩增，它的许多插入应该是多态的，因此可以作为近期种群历史的遗传特征。到目前为止，我们已经从3个不同种族的代表中克隆出286个含有ta1的基因座。我们对其中的201个进行了评估，发现至少95个是多态的。其中56个（57%）是新的插入，因为它们不存在于当前的人类数据库中。有趣的是，这些多态性中有14个是他们克隆的个体所独有的，我们现在正在研究它们在每个相关种族群体中的分布。我们的研究结果表明，大多数曾经含有潜在活性（即全长，FL）祖先L1元件的遗传位点现在已在现代人中不再存在。这些FL L1元件代表了4个不同的L1家族（L1PA2-L1PA5），从8 - 25 MYA之间扩增。因此，对这些活性L1元素进行了持续的纯化选择。这意味着不仅祖先活跃的L1元件对早期人类施加了显著的遗传负荷，而且目前活跃的Ta家族也可能如此。为了理解为什么新的L1家族不断出现并取代现有的家族，我们确定了上述4个祖先家族中每个家族进化特征的核苷酸变化。我们发现ORF1的一个区域经历了一段积极（适应性）选择，然后停止。适应性进化涉及ORF1的一个区域，其他人（使用小鼠L1）表明该区域参与蛋白质-蛋白质相互作用。适应性进化的这一阶段可能代表了对元素或宿主其他地方的进化变化的适应。在后者的情况下，可能涉及对L1复制所需的宿主因子的适应或通过宿主抑制。目前正在进行实验来测试所有这些可能性。

Mammalian L1 elements (LINE-1) replicate (retrotranspose) by copying their RNA transcripts into DNA which is then integrated into the genome. L1 elements have been replicating and evolving in mammalian genomes since before the mammalian radiation 100 MYA. L1 elements account for 17% of the human genome and cause up to 0.2% of the genetic defects. In addition, they likely catalyze the retroposition of the highly repeated SINE (Alu) families and processed pseudogenes. The ~6 kb human L1 element has four regions: A 5? UTR (untranslated region) has a regulatory function; ORF I encodes an RNA binding protein; ORF II encodes the L1 cDNA replicase; the 3? UTR contains a conserved G-rich polypurine motif. We found that both rodent and human L1 elements evolve rapidly with novel families continually replacing older ones. Since most of the copies of past L1 families are retained, modern genomes contain both ancestral and modern L1 families. The relics of the extinct L1 families can yield phylogenetic information about the host species and important genetic parameters such as its neutral mutation rate. L1 insertions generated by currently replicating families provide robust polymorphic genetic markers for analyzing population structure. We continued our analysis of the human Ta L1 family focusing on isolating the insertions produced its Ta1 subfamily which we recently discovered. Since this family is currently amplifying in humans, many of its inserts should be polymorphic and thus useful as genetic characters for recent population history. So far we have cloned 286 Ta1-containing loci from a representative of 3 different ethnic groups. We were able to evaluate 201 of them and found that at least 95 were polymorphic. Of these 56 (57%) are novel inserts since they are not present in the current human data base. Interestingly, 14 of these polymorphisms are unique to the individual from whom they were cloned and we are now examining their distribution within each relevant ethnic group. Our results showing that most of the genetic loci that once contained potentially active (i.e., full length, FL) ancestral L1 elements are no longer present in modern humans has now been published. These FL L1 elements represented four different L1 families (L1PA2-L1PA5) that amplified from between 8 and 25 MYA. Thus, there has been continual purifying selection against these active L1 elements. This implies that not only did the ancestral active L1 elements impose a significant genetic load on early humans, but that the currently active Ta family may also do so. In an attempt to understand why novel L1 families continually arise and replace existing families, we determined the nucleotide changes that characterized the evolution of each of the 4 ancestral families mentioned above. We found that a region of ORF1 underwent an episode of positive (adaptive) selection which then ceased. The adaptive evolution involves a region of ORF1 shown by others (using mice L1) to be involved in protein-protein interaction. This episode of adaptive evolution could represent an accommodation to evolutionary changes elsewhere in the element or in the host. In case of the latter, adaptation to a host factor required for L1 replication or to by pass host repression could be involved. Experiments are now underway to test all of these possibilities.