Functional noncoding sequences derived from SINEs in the mammalian genome
Functional noncoding sequences derived from SINEs in the mammalian genome
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DOI：
10.1101/gr.5255506
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发表时间：
2006-07-01
期刊：
影响因子：
7
通讯作者：
Okada, Norihiro
中科院分区：
文献类型：
--
作者：
Nishihara, Hidenori;Smit, Arian F. A.;Okada, Norihiro
最近对哺乳动物序列的比较分析表明，大量非蛋白质编码基因组区域受到强烈的选择性限制。在这里，我们报告其中一些基因座源自新定义的古代 SINE（短散布重复元件）家族。这是一个令人惊讶的结果，因为 SINE 和其他转座元件通常被认为是基因组寄生虫。我们将古老的 SINE 家族命名为 AmnSINE1，即 Amniota SINE1，因为我们发现它也存在于哺乳动物和鸟类中，并且其中一些副本早于 3.1 亿年前的哺乳动物-鸟类分裂 (Mya)。 AmnSINE1 具有 5S rRNA 和 tRNA 衍生的 SINE 的嵌合结构，并且与我们在腔棘鱼、角鲨、盲鳗和文昌鱼基因组中表征的 5 个 tRNA 衍生的 SINE 家族相关。所有新描述的 SINE 家族都有一个共同的中心结构域，斑马鱼 SINE3 也共享该结构域，我们将它们统称为 DeuSINE (Deuterostomia SINE) 超家族。值得注意的是，在人类基因组中仍可识别的大约 1000 个 AmnSINE1 拷贝中，有 105 个对应于哺乳动物直向同源物中在系统发育上高度保守的位点。中心域的保护最强。因此，AmnSINE1 似乎是转座元件的最佳例子，其中很大一部分拷贝已经获得了基因组功能。
Recent comparative analyses of mammalian sequences have revealed that a large number of nonprotein-coding genomic regions are under strong selective constraint. Here, we report that some of these loci have been derived from a newly defined family of ancient SINEs ( short interspersed repetitive elements). This is a surprising result, as SINEs and other transposable elements are commonly thought to be genomic parasites. We named the ancient SINE family AmnSINE1, for Amniota SINE1, because we found it to be present in mammals as well as in birds, and some copies predate the mammalian-bird split 310 million years ago (Mya). AmnSINE1 has a chimeric structure of a 5S rRNA and a tRNA-derived SINE, and is related to five tRNA-derived SINE families that we characterized here in the coelacanth, dogfish shark, hagfish, and amphioxus genomes. All of the newly described SINE families have a common central domain that is also shared by zebrafish SINE3, and we collectively name them the DeuSINE (Deuterostomia SINE) superfamily. Notably, of the similar to 1000 still identifiable copies of AmnSINE1 in the human genome, 105 correspond to loci phylogenetically highly conserved among mammalian orthologs. The conservation is strongest over the central domain. Thus, AmnSINE1 appears to be the best example of a transposable element of which a significant fraction of the copies have acquired genomic functionality.