Luchetti Andrea, Plazzi Federico, Mantovani Barbara
Dipartimento di Scienze Biologiche, Geologiche e Ambientali - Università di Bologna, Italy.
Genome Biol Evol. 2017 Jun 1;9(6):1406-17. doi: 10.1093/gbe/evx094.
Short interspersed elements (SINEs) are non-autonomous retrotransposons. Although they usually show fast evolutionary rates, in some instances highly conserved domains (HCDs) have been observed in elements with otherwise divergent sequences and from distantly related species. Here, we document the life history of two HCD-SINE families in the elephant shark Callorhinchus milii, one specific to the holocephalan lineage (CmiSINEs) and another one (SacSINE1-CM) with homologous elements in sharks and the coelacanth (SacSINE1s, LmeSINE1s). The analyses of their relationships indicated that these elements share the same 3'-tail, which would have allowed both elements to rise to high copy number by exploiting the C. milii L2-2_CM long interspersed element (LINE) enzymes. Molecular clock analysis on SINE activity in C. milii genome evidenced two replication bursts occurring right after two major events in the holocephalan evolution: the end-Permian mass extinction and the radiation of modern Holocephali. Accordingly, the same analysis on the coelacanth homologous elements, LmeSINE1, identified a replication wave close to the split age of the two extant Latimeria species. The genomic distribution of the studied SINEs pointed out contrasting results: some elements were preferentially sorted out from gene regions, but accumulated in flanking regions, while others appear more conserved within genes. Moreover, data from the C. milii transcriptome suggest that these SINEs could be involved in miRNA biogenesis and may be targets for miRNA-based regulation.
短散在元件（SINEs）是非自主逆转座子。尽管它们通常显示出快速的进化速率，但在某些情况下，在序列其他部分存在差异且来自远缘物种的元件中也观察到了高度保守结构域（HCDs）。在这里，我们记录了象鲨Callorhinchus milii中两个HCD-SINE家族的生命史，一个是全头类谱系特有的（CmiSINEs），另一个（SacSINE1-CM）在鲨鱼和腔棘鱼中有同源元件（SacSINE1s、LmeSINE1s）。对它们关系的分析表明，这些元件共享相同的3'尾，这使得两个元件都能够通过利用Callorhinchus milii的L2-2_CM长散在元件（LINE）酶增加到高拷贝数。对Callorhinchus milii基因组中SINE活性的分子钟分析证明，在全头类进化的两个主要事件之后紧接着发生了两次复制爆发：二叠纪末大灭绝和现代全头类的辐射。因此，对腔棘鱼同源元件LmeSINE1进行的相同分析确定了一次接近两个现存矛尾鱼物种分化时代的复制波。所研究的SINEs的基因组分布指出了不同的结果：一些元件优先从基因区域中被分选出来，但在侧翼区域积累，而其他元件在基因内似乎更保守。此外，来自Callorhinchus milii转录组的数据表明，这些SINEs可能参与miRNA生物合成，并且可能是基于miRNA调控的靶标。
