Discovery of Novel Genes Derived from Transposable Elements Using Integrative Genomic Analysis
Discovery of Novel Genes Derived from Transposable Elements Using Integrative Genomic Analysis
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DOI：
10.1093/molbev/msv042
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发表时间：
2015-06-01
影响因子：
10.7
通讯作者：
Bureau, Thomas E.
中科院分区：
文献类型：
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作者：
Hoen, Douglas R.;Bureau, Thomas E.
复杂的真核生物含有数百万个转座因子（TE），构成其核基因组的大部分。TE由结构、调节和编码序列组成，这些序列通常与转座相关，但偶尔赋予生物体选择优势，从而可能变得脱适。Exapted transposable element genes（ETEs）在从脊椎动物的适应性免疫到植物的发育过程中发挥着重要的作用。然而，尽管它们具有明显的重要性，但大多数ETE都是偶然发现的，很少进行系统的搜索，这表明可能还有更多的ETE有待发现。为了探索这种可能性，我们开发了一个全面系统的方法来寻找ETE。我们使用TE特异性保守结构域来高精度地识别来自TE的基因，并基于其与已知ETEs、常规（非TE）基因和TE基因的参考集的相似性来筛选它们的外适应特征，所述参考集跨越不同的遗传属性，包括重复性、基因组位置和序列的保守性以及表达水平和抑制性小RNA。应用这种方法在模式植物拟南芥，我们发现了一个令人惊讶的大量的新的高置信度ETEs。有趣的是，与已知的植物ETE不同，几个新的埃特家族形成串联排列的基因簇，而其他家族则相对年轻。我们的研究结果不仅确定了可能具有实际应用的新的TE衍生基因，而且还挑战了TE外适应仅仅是古代生命遗迹的概念，而是表明它可能继续从根本上推动进化。
Complex eukaryotes contain millions of transposable elements (TEs), comprising large fractions of their nuclear genomes. TEs consist of structural, regulatory, and coding sequences that are ordinarily associated with transposition, but that occasionally confer on the organism a selective advantage and may thereby become exapted. Exapted transposable element genes (ETEs) are known to play critical roles in diverse systems, from vertebrate adaptive immunity to plant development. Yet despite their evident importance, most ETEs have been identified fortuitously and few systematic searches have been conducted, suggesting that additional ETEs may await discovery. To explore this possibility, we develop a comprehensive systematic approach to searching for ETEs. We use TE-specific conserved domains to identify with high precision genes derived from TEs and screen them for signatures of exaptation based on their similarities to reference sets of known ETEs, conventional (non-TE) genes, and TE genes across diverse genetic attributes including repetitiveness, conservation of genomic location and sequence, and levels of expression and repressive small RNAs. Applying this approach in the model plant Arabidopsis thaliana, we discover a surprisingly large number of novel high confidence ETEs. Intriguingly, unlike known plant ETEs, several of the novel ETE families form tandemly arrayed gene clusters, whereas others are relatively young. Our results not only identify novel TE-derived genes that may have practical applications but also challenge the notion that TE exaptation is merely a relic of ancient life, instead suggesting that it may continue to fundamentally drive evolution.