Adelson David L, Raison Joy M, Edgar Robert C
School of Molecular and Biomedical Science, University of Adelaide, North Terrace, Adelaide, South Australia, 5005, Australia.
Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12855-60. doi: 10.1073/pnas.0901282106. Epub 2009 Jul 22.
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.
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充分的表征。牛基因组包含典型的真兽类哺乳动物重复序列，但也有大量长散布核元件RTE（BovB）元件，据推测这些元件是从有鳞目水平转移而来的。我们对BovB重复序列的分析表明，目前它们中只有少数可能在牛中发生逆转录转座。然而，牛L1重复序列（L1BT）有许多可能活跃的拷贝。BovB和L1BT替代率的比较表明，L1BT是一个比BovB更年轻的重复序列家族。与小鼠和人类不同，L1的出现与G+C含量没有负相关。然而，BovB、Bov A2、ART2A和Bov-tA与G+C呈负相关，尽管Bov-tA的相关性较弱。此外，通过对散布重复序列和简单序列重复序列进行全基因组相关性分析，我们已经根据重复序列含量确定了基因组区域，这些区域似乎定义了祖先基因组区域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在很大程度上是保守的。
