Pace John K, Feschotte Cédric
Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA.
Genome Res. 2007 Apr;17(4):422-32. doi: 10.1101/gr.5826307. Epub 2007 Mar 5.
Class 2, or DNA transposons, make up approximately 3% of the human genome, yet the evolutionary history of these elements has been largely overlooked and remains poorly understood. Here we carried out the first comprehensive analysis of the activity of human DNA transposons over the course of primate evolution using three independent computational methods. First, we conducted an exhaustive search for human DNA transposons nested within L1 and Alu elements known to be primate specific. Second, we assessed the presence/absence of 794 human DNA transposons at orthologous positions in 10 mammalian species using sequence data generated by The ENCODE Project. These two approaches, which do not rely upon sequence divergence, allowed us to classify DNA transposons into three different categories: anthropoid specific (40-63 My), primate specific (64-80 My), and eutherian wide (81-150 My). Finally, we used this data to calculate the substitution rates of DNA transposons for each category and refine the age of each family based on the average percent divergence of individual copies to their consensus. Based on these combined methods, we can confidently estimate that at least 40 human DNA transposon families, representing approximately 98,000 elements ( approximately 33 Mb) in the human genome, have been active in the primate lineage. There was a cessation in the transpositional activity of DNA transposons during the later phase of the primate radiation, with no evidence of elements younger than approximately 37 My. This data points to intense activity of DNA transposons during the mammalian radiation and early primate evolution, followed, apparently, by their mass extinction in an anthropoid primate ancestor.
第2类，即DNA转座子，约占人类基因组的3%，然而这些元件的进化历史在很大程度上被忽视了，人们对其了解仍然很少。在这里，我们使用三种独立的计算方法，对灵长类动物进化过程中人类DNA转座子的活性进行了首次全面分析。首先，我们对嵌套在已知为灵长类动物特有的L1和Alu元件中的人类DNA转座子进行了详尽搜索。其次，我们利用由ENCODE计划生成的序列数据，评估了10种哺乳动物直系同源位置上794个人类DNA转座子的存在与否。这两种方法不依赖于序列差异，使我们能够将DNA转座子分为三类：类人猿特有的（4000 - 6300万年前）、灵长类动物特有的（6400 - 8000万年前）和真兽类广泛存在的（8100 - 15000万年前）。最后，我们利用这些数据计算了每一类DNA转座子的替代率，并根据单个拷贝与其共有序列的平均差异百分比来细化每个家族的年龄。基于这些综合方法，我们可以有把握地估计，在灵长类动物谱系中，至少有40个人类DNA转座子家族是活跃的，这些家族在人类基因组中约有98000个元件（约33兆碱基）。在灵长类动物辐射的后期阶段，DNA转座子的转座活性停止了，没有证据表明存在年龄小于约3700万年前的元件。这些数据表明，在哺乳动物辐射和早期灵长类动物进化过程中，DNA转座子具有强烈的活性，随后，显然在一个类人猿灵长类祖先中大量灭绝。
