MAMMALIAN TRANSPOSONS

哺乳动物L1元件（LINE-1）通过将其RNA转录物复制（反转录转座）到DNA中，然后将DNA整合到基因组中。早在哺乳动物辐射之前的1亿年，L1元件就已经在哺乳动物基因组中复制和进化，现在占某些基因组的20%。在人类中，L1反转录转座导致高达0.2%的遗传缺陷。L1元件的长度约为7 kb，由4个区域组成：5' UTR（非翻译区）具有调控功能; ORF I编码RNA结合蛋白; ORF II编码L1 cDNA复制酶; 3' UTR含有一个保守的富含G的多嘌呤基序，可形成复杂的链内DNA和RNA结构。我们发现，啮齿动物和人类的L1元素进化迅速，新的家庭不断取代旧的。由于过去L1家族的大部分拷贝被保留下来，现代基因组包含祖先和现代L1家族。除此之外，已灭绝的L1家族的遗迹可以提供有关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。目前复制家庭产生的L1插入提供了强大的多态性遗传标记，用于分析人口结构。去年，我们报告了我们对人类Ta L1家族的分析。这个家族在人类和黑猩猩谱系分裂后不久就出现了约400万年，并迅速扩大，演变成几个亚家族：Ta-0和Ta-1。总体而言，约50%的Ta插入在人群中是多态性的，并且由Ta-1的最年轻子集Ta-1d产生的插入中超过90%是多态性的。事实上，所有12个记录在案的由L1插入引起的遗传缺陷（其中一些发生在子宫内）都是由于Ta，10个是由于Ta-1d插入。因此，新的Ta L1插入增加了人类的遗传多样性。此后我们发现，大多数曾经含有潜在活性的遗传基因座（即，全长，FL）祖先的L1元件不再存在于现代人类。这些FL L1元件代表4个不同的L1家族，从5和15 MYA之间扩增。因此，一直存在针对这些活性L1元件的持续净化选择。这强烈地暗示，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家族也是如此。这种遗传负荷的性质目前正在研究中。我们还比较了这四个祖先人类L1家族内的序列差异。我们的研究结果提供了第一个明确的和统计学上可靠的证据，证明男性的突变率高于女性。这是首次提出的Halflies超过50年前，尽管相当大的努力，结果仍然是矛盾的。我们的研究结果对分子进化和物种形成具有深远的意义，并为评估给定人类基因座的遗传变化率提供了基线突变率。鉴于遗传多态性对遗传作图和群体遗传学的重要性，我们启动了一个特殊的项目，以分离由Ta-1 L1亚家族的转座活性引起的各种人群中的所有多态性位点。第一阶段（从四个不同的人群中分离多态性基因座）现在已经足够先进，我们已经开始与几个非NIH机构合作，使用我们目前确定的基因座来分析几个人群的遗传组成。我们将很快实施使用L1标记来绘制与疾病状态相关的遗传性状。我们预计在大约6个月内开始第二阶段。在这里，我们将使用从第一阶段获得的信息，以确定额外的多态性L1位点从其他人群或个人，以及开发一种测定转座率。

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 and now account for as much as 20% of some genomes. In humans L1 retrotransposition causes up to 0.2% of the genetic defects. The ~7 kb L1 element has four regions: The 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 which can form complex intrastrand DNA and RNA structures. 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. Among other things, the relics of 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. Last year we reported on our analysis of the human Ta L1 family. This family arose ~4 MYA soon after the human and chimpanzee lineages split and has been amplifying rapidly, evolving into several subfamilies: Ta-0 and Ta-1. Overall, about 50% of Ta insertions are polymorphic across human populations and more than 90% of the inserts generated by Ta-1d, the youngest subset of Ta-1, are polymorphic. Indeed all 12 documented genetic defects caused by L1 insertions (some of which occurred in utero) are due to Ta, 10 by Ta-1d insertions. Thus novel Ta L1 insertions are increasing the genetic diversity of humans. We have since found 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. These FL L1 elements represented four different L1 families that amplified from between 5 and 15 MYA. Thus, there has been continual purifying selection against these active L1 elements. This strongly 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 also does. The nature of this genetic load in now being investigated. We also compared sequence divergence within these four ancestral human L1 families. Our results provided the first unequivocal and statistically robust evidence that the human mutation rate is higher in males than in females. This was first proposed by Haldane over 50 years ago and despite considerable effort the results remained contradictory. Our results have profound implications for molecular evolution and speciation and provide a base line mutational rate for evaluating the rate of genetic change of given human loci. Given the importance of genetic polymorphisms for genetic mapping and population genetics we had initiated a special project to isolate all of the polymorphic loci in various human populations caused by the transpositional activity of the Ta-1 L1 subfamily. Phase I (the isolation of polymorphic loci from four different human populations) is now sufficiently advanced that we have initiated collaborations with several non-NIH institutions to use our presently identified loci to analyze the genetic composition of several human populations. We will soon implement the use of the L1 markers for mapping genetic traits related to disease states. We anticipate beginning phase II in about 6 months. Here we will use the information gained from phase I to identify additional polymorphic L1 loci from additional populations or individuals as well as to develop an assay for transposition rate.