Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain.
RNA. 2014 Jul;20(7):959-76. doi: 10.1261/rna.044560.114. Epub 2014 May 21.
Our genome contains tens of thousands of long noncoding RNAs (lncRNAs), many of which are likely to have genetic regulatory functions. It has been proposed that lncRNA are organized into combinations of discrete functional domains, but the nature of these and their identification remain elusive. One class of sequence elements that is enriched in lncRNA is represented by transposable elements (TEs), repetitive mobile genetic sequences that have contributed widely to genome evolution through a process termed exaptation. Here, we link these two concepts by proposing that exonic TEs act as RNA domains that are essential for lncRNA function. We term such elements Repeat Insertion Domains of LncRNAs (RIDLs). A growing number of RIDLs have been experimentally defined, where TE-derived fragments of lncRNA act as RNA-, DNA-, and protein-binding domains. We propose that these reflect a more general phenomenon of exaptation during lncRNA evolution, where inserted TE sequences are repurposed as recognition sites for both protein and nucleic acids. We discuss a series of genomic screens that may be used in the future to systematically discover RIDLs. The RIDL hypothesis has the potential to explain how functional evolution can keep pace with the rapid gene evolution observed in lncRNA. More practically, TE maps may in the future be used to predict lncRNA function.
我们的基因组包含数以万计的长非编码 RNA(lncRNA),其中许多可能具有遗传调控功能。有人提出,lncRNA 可以组合成离散的功能域,但这些功能域的性质及其鉴定仍然难以捉摸。一类在 lncRNA 中丰富的序列元件是转座元件(TEs),它们是重复的移动遗传序列,通过一种称为适应的过程广泛参与了基因组进化。在这里,我们通过提出外显子 TEs 作为 lncRNA 功能所必需的 RNA 结构域,将这两个概念联系起来。我们将这些元素称为长非编码 RNA 的重复插入结构域(RIDLs)。越来越多的 RIDLs 已经通过实验定义,其中 lncRNA 的 TE 衍生片段充当 RNA、DNA 和蛋白质结合结构域。我们提出,这些反映了 lncRNA 进化过程中适应的更普遍现象,其中插入的 TE 序列被重新用作蛋白质和核酸的识别位点。我们讨论了一系列未来可能用于系统发现 RIDLs 的基因组筛选。RIDL 假说有可能解释功能进化如何跟上 lncRNA 中观察到的快速基因进化。更实际的是,TE 图谱将来可能用于预测 lncRNA 的功能。