Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants.
Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants.
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DOI：
10.1371/journal.pgen.1006630
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发表时间：
2017-02
期刊：
影响因子：
4.5
通讯作者：
Mirouze M
中科院分区：
文献类型：
--
作者：
Lanciano S;Carpentier MC;Llauro C;Jobet E;Robakowska-Hyzorek D;Lasserre E;Ghesquière A;Panaud O;Mirouze M
反转录转座子是植物和动物基因组中丰富的移动的遗传元件。虽然它们被表观遗传机制有效地沉默，但它们可以在压力下或在发育过程中重新激活。它们的转录水平不能反映它们的转座能力，因此很难评估它们对活性活动组的贡献。在这里，我们应用了一种基于活性逆转录转座子的染色体外环状DNA（eccDNA）形式的高通量测序的简单方法来表征植物中移动的逆转录转座子的库。该方法成功地鉴定了拟南芥和水稻材料中已知的活性反转录转座子，其中表观基因组不稳定。当将mobilome-seq应用于野生型水稻的发育阶段时，我们将PopRice鉴定为在野生型胚乳中产生eccDNA形式的高活性反转录转座子。mobilome-seq策略为表征植物基因组中尚未探索的部分开辟了新的途径。长期以来被认为是“垃圾DNA”，转座因子（TE）的进化力量现在已经得到了很好的建立，并且TE对真核生物基因组的可塑性有很大的贡献。然而，很难完全表征基因组的移动的部分或活性移动组，并且跟踪TE活性仍然具有挑战性。因此，我们建议使用染色体外环状DNA的检测作为诊断植物TE活动。我们的mobilome-seq技术允许在野生型水稻种子中鉴定一种新的活性反转录转座子，并将代表表征TE的体细胞活性的强有力策略，以评估其对基因组稳定性的影响，并更好地了解其在多细胞真核生物中的适应能力。
Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants. This method successfully identified known active retrotransposons in both Arabidopsis and rice material where the epigenome is destabilized. When applying mobilome-seq to developmental stages in wild type rice, we identified PopRice as a highly active retrotransposon producing eccDNA forms in the wild type endosperm. The mobilome-seq strategy opens new routes for the characterization of a yet unexplored fraction of plant genomes. Long time considered as « junk DNA », the evolutive force of transposable elements (TEs) is now well established and TEs contribute strongly to eukaryote genome plasticity. However, it is difficult to fully characterize the mobile part of a genome, or active mobilome, and tracking TE activity remains challenging. We therefore propose to use the detection of extrachromosomal circular DNA as a diagnostic for plant TE activity. Our mobilome-seq technique allowed to identify a new active retrotransposon in wild type rice seeds, and will represent a powerful strategy in characterizing the somatic activity of TEs to evaluate their impact on genome stability and to better understand their adaptive capacity in multicellular eukaryotes.