Evolutionary history of mammalian transposons determined by genome-wide defragmentation.
Evolutionary history of mammalian transposons determined by genome-wide defragmentation.
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DOI：
10.1371/journal.pcbi.0030137
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发表时间：
2007-07
影响因子：
4.3
通讯作者：
Warburton PE
中科院分区：
文献类型：
--
作者：
Giordano J;Ge Y;Gelfand Y;Abrusán G;Benson G;Warburton PE
转座因子（te）对哺乳动物基因组的持续轰击导致te至少占人类基因组的45%。由于它们年龄大、数量多，因此在比较系统基因组学中具有重要意义。然而，以前对TE年龄的估计是基于衍生的一致序列或系统发育分析的分歧，这可能是不可靠的，特别是对于更古老的更分歧的元素。因此，对TE的组织和片段进行了一种新的全基因组分析，以估计TE的年龄，而不依赖于序列组成和分化或恒定分子钟的假设。对人类基因组中te的分析揭示了约60万个te转位成其他te并片段化的例子，覆盖了所有te的40%或约542 Mbp的基因组序列。这些te在进化过程中的相对年龄在它们的组织中是隐含的，因为新的te必然会转化为已经存在的较老的te。构建了每个TE转换到其他TE的次数矩阵，并开发了一个新的目标函数，该函数推导了人类TE的时间顺序和相对年龄，跨度为1亿至1亿年。这种方法已经被用来推断所有四种主要TE类的相对年龄，包括最古老、最分散的元素。对人类基因组历史上的DNA转座子的分析揭示了一些MER2转座子的早期活性，以及灵长类谱系中MER1转座子的相对较近的活性。对另外6种哺乳动物基因组的te进行了整理和分析。对这些哺乳动物基因组中te独立时间顺序的两两比较揭示了物种系统发育，基因组之间共享的转座子比物种特异性转座子更古老，以及在物种形成期间可能活跃的te子集。转座因子（te）是分散的重复DNA家族，能够从一个地方复制到另一个地方；在进化过程中，它们确实侵染了我们的基因组，现在构成了我们总DNA的45%。由于它们存在的时间长且数量多，因此te在进化基因组学中很重要。然而，根据DNA序列组成来估计它们的年龄是不可靠的，特别是对于更古老、更分散的元素。因此，基于以下事实，开发了一种估算TEs年龄的新方法：当te在整个基因组中扩散时，它们插入并碎片化已经存在的较老te。因此，te的年龄可以通过它们在进化过程中破碎的频率来揭示。我们对te进行了全基因组的碎片整理，并开发了一个新的目标函数，以获得跨越bbb - 1亿年的te的时间顺序。该方法已用于从7个已测序的哺乳动物基因组中推断TE的相对年龄，包括所有4个主要TE类别，包括最古老，最分化的元素。这种年龄估计与TE序列组成或分化无关，也不依赖于恒定分子钟的假设。这项研究为哺乳动物基因组中一些最丰富和最古老的重复DNA元素的进化史提供了一种新的分析，这对于理解在进化过程中塑造我们基因组的动力是重要的。
The constant bombardment of mammalian genomes by transposable elements (TEs) has resulted in TEs comprising at least 45% of the human genome. Because of their great age and abundance, TEs are important in comparative phylogenomics. However, estimates of TE age were previously based on divergence from derived consensus sequences or phylogenetic analysis, which can be unreliable, especially for older more diverged elements. Therefore, a novel genome-wide analysis of TE organization and fragmentation was performed to estimate TE age independently of sequence composition and divergence or the assumption of a constant molecular clock. Analysis of TEs in the human genome revealed ∼600,000 examples where TEs have transposed into and fragmented other TEs, covering >40% of all TEs or ∼542 Mbp of genomic sequence. The relative age of these TEs over evolutionary time is implicit in their organization, because newer TEs have necessarily transposed into older TEs that were already present. A matrix of the number of times that each TE has transposed into every other TE was constructed, and a novel objective function was developed that derived the chronological order and relative ages of human TEs spanning >100 million years. This method has been used to infer the relative ages across all four major TE classes, including the oldest, most diverged elements. Analysis of DNA transposons over the history of the human genome has revealed the early activity of some MER2 transposons, and the relatively recent activity of MER1 transposons during primate lineages. The TEs from six additional mammalian genomes were defragmented and analyzed. Pairwise comparison of the independent chronological orders of TEs in these mammalian genomes revealed species phylogeny, the fact that transposons shared between genomes are older than species-specific transposons, and a subset of TEs that were potentially active during periods of speciation. Transposable elements (TEs) are interspersed repetitive DNA families that are capable of copying themselves from place to place; they have literally infested our genome over evolutionary time, and now comprise as much as 45% of our total DNA. Because of their great age and abundance, TEs are important in evolutionary genomics. However, estimates of their age based on DNA sequence composition have been unreliable, especially for older more diverged elements. Therefore, a novel method to estimate the age of TEs was developed based on the fact that as TEs spread throughout the genome, they inserted into and fragmented older TEs that were already present. Therefore, the age of TEs can be revealed by how often they have been fragmented over evolutionary time. We performed a genome-wide defragmention of TEs, and developed a novel objective function to derive the chronological order of TEs spanning >100 million years. This method has been used to infer the relative ages of TEs from seven sequenced mammalian genomes across all four major TE classes, including the oldest, most diverged elements. This age estimate is independent of TE sequence composition or divergence and does not rely on the assumption of a constant molecular clock. This study provides a novel analysis of the evolutionary history of some of the most abundant and ancient repetitive DNA elements in mammalian genomes, which is important for understanding the dynamic forces that shape our genomes during evolution.
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影响因子：
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