Massively parallel jumping assay decodes Alu retrotransposition activity.
Massively parallel jumping assay decodes Alu retrotransposition activity.
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大规模并行跳跃测定解码 Alu 逆转录转座活性。
DOI：
10.1101/2024.04.16.589814
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发表时间：
2024
期刊：
影响因子：
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通讯作者：
Ahituv,Nadav
中科院分区：
文献类型：
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作者：
Matharu,Navneet;Zhao,Jingjing;Sohota,Ajuni;Deng,Linbei;Hung,Yan;Li,Zizheng;Sims,Jasmine;Rattanasopha,Sawitree;Meyer,Josh;Carbone,Lucia;Kircher,Martin;Ahituv,Nadav
人类基因组包含数百万个沉默的反转录转座子拷贝，但其中许多拷贝如果发生突变，可能会变得活跃，从而产生包括疾病在内的表型后果。然而，对于逆转录转座子的核苷酸变化如何影响其跳跃活性，目前还没有完全了解。在这里，我们开发了一种大规模平行跳跃实验（MPJA）来测试成千上万个转座子的跳跃潜力。我们生成了包含165,087种不同单倍型的四个Alu反转录转座子的核苷酸变异文库，并使用MPJA测试了它们的跳跃能力。我们发现了66,821种独特的跳跃单倍型，这使我们能够确定对转位至关重要的结构域和变异。将这些变异映射到Alu-RNA二级结构，揭示了有助于跳跃潜力的茎环特征。综上所述，我们的工作提供了一种高通量的分析方法，可以评估逆转录转座子跳跃的能力，并识别人类基因组中有可能重新激活它们的核苷酸变化。
The human genome contains millions of copies of retrotransposons that are silenced but many of these copies have potential to become active if mutated, having phenotypic consequences, including disease. However, it is not thoroughly understood how nucleotide changes in retrotransposons affect their jumping activity. Here, we develop a massively parallel jumping assay (MPJA) that tests the jumping potential of thousands of transposons en masse. We generate a nucleotide variant library of four Alu retrotransposons containing 165,087 different haplotypes and test them for their jumping ability using MPJA. We found 66,821 unique jumping haplotypes, allowing us to pinpoint domains and variants vital for transposition. Mapping these variants to the Alu-RNA secondary structure revealed stem-loop features that contribute to jumping potential. Combined, our work provides a high-throughput assay that assesses the ability of retrotransposons to jump and identifies nucleotide changes that have the potential to reactivate them in the human genome.