National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD , USA.
Department of Genetics, Institute for Quantitative Biomedical Sciences, Geisel School of Medicine, Dartmouth College , Hanover, NH , USA.
Front Bioeng Biotechnol. 2015 Jun 9;3:71. doi: 10.3389/fbioe.2015.00071. eCollection 2015.
Transposable elements (TEs) are abundant in mammalian genomes and appear to have contributed to the evolution of their hosts by providing novel regulatory or coding sequences. We analyzed different regions of long intergenic non-coding RNA (lincRNA) genes in human and mouse genomes to systematically assess the potential contribution of TEs to the evolution of the structure and regulation of expression of lincRNA genes. Introns of lincRNA genes contain the highest percentage of TE-derived sequences (TES), followed by exons and then promoter regions although the density of TEs is not significantly different between exons and promoters. Higher frequencies of ancient TEs in promoters and exons compared to introns implies that many lincRNA genes emerged before the split of primates and rodents. The content of TES in lincRNA genes is substantially higher than that in protein-coding genes, especially in exons and promoter regions. A significant positive correlation was detected between the content of TEs and evolutionary rate of lincRNAs indicating that inserted TEs are preferentially fixed in fast-evolving lincRNA genes. These results are consistent with the repeat insertion domains of LncRNAs hypothesis under which TEs have substantially contributed to the origin, evolution, and, in particular, fast functional diversification, of lincRNA genes.
转座元件（TEs）在哺乳动物基因组中大量存在，通过提供新的调控或编码序列，似乎为宿主的进化做出了贡献。我们分析了人类和小鼠基因组中长基因间非编码 RNA（lincRNA）基因的不同区域，以系统评估 TEs 对 lincRNA 基因结构和表达调控进化的潜在贡献。lincRNA 基因的内含子包含最高百分比的 TE 衍生序列（TES），其次是外显子，然后是启动子区域，尽管外显子和启动子之间的 TE 密度没有显著差异。与内含子相比，启动子和外显子中古老 TE 的频率更高，这意味着许多 lincRNA 基因在灵长类动物和啮齿动物分化之前就已经出现。TES 在 lincRNA 基因中的含量明显高于蛋白质编码基因，尤其是在外显子和启动子区域。我们检测到 TES 含量与 lincRNA 进化率之间存在显著的正相关，表明插入的 TEs 优先在快速进化的 lincRNA 基因中固定下来。这些结果与 LncRNAs 的重复插入区域假说一致，该假说认为 TEs 为 lincRNA 基因的起源、进化，特别是快速功能多样化做出了重大贡献。
