Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome
Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome
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DOI：
10.1073/pnas.0901282106
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发表时间：
2009-08-04
影响因子：
11.1
通讯作者：
Edgar, Robert C.
中科院分区：
文献类型：
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作者：
Adelson, David L.;Raison, Joy M.;Edgar, Robert C.
哺乳动物中散布重复序列的组成和分布在人类和小鼠基因组中得到了最好的表征。牛基因组包含典型的真兽类哺乳动物重复序列，而且还具有大量长散布核元件 RTE (BovB) 元件，推测是从鳞状动物水平转移的。我们对 BovB 重复序列的分析表明，目前只有少数重复序列可能在牛体内逆转座。然而，牛 L1 重复序列 (L1 BT) 有许多可能的活性拷贝。 BovB 和 L1 BT 替代率的比较表明，L1 BT 是比 BovB 更年轻的重复家族。与小鼠和人类相比，L1 的出现与 G+C 含量不呈负相关。然而，BovB、Bov A2、ART2A 和 Bov-tA 与 G+C 呈负相关，尽管 Bov-tAs 相关性较弱。此外，通过对散布的和简单的序列重复进行全基因组相关性分析，我们通过重复内容识别了基因组区域，这些重复内容似乎定义了祖先与反刍动物特异性基因组区域。这些富含 L2 和 MIR 重复序列的祖先区域在牛和人类之间很大程度上是保守的。
Interspersed repeat composition and distribution in mammals have been best characterized in the human and mouse genomes. The bovine genome contains typical eutherian mammal repeats, but also has a significant number of long interspersed nuclear element RTE (BovB) elements proposed to have been horizontally transferred from squamata. Our analysis of the BovB repeats has indicated that only a few of them are currently likely to retrotranspose in cattle. However, bovine L1 repeats (L1 BT) have many likely active copies. Comparison of substitution rates for BovB and L1 BT indicates that L1 BT is a younger repeat family than BovB. In contrast to mouse and human, L1 occurrence is not negatively correlated with G+C content. However, BovB, Bov A2, ART2A, and Bov-tA are negatively correlated with G+C, although Bov-tAs correlation is weaker. Also, by performing genome wide correlation analysis of interspersed and simple sequence repeats, we have identified genome territories by repeat content that appear to define ancestral vs. ruminant-specific genomic regions. These ancestral regions, enriched with L2 and MIR repeats, are largely conserved between bovine and human.