Denisko Danielle, Kim Jeonghyeon, Ku Jayoung, Zhao Boxun, Lee Eunjung Alice
Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
bioRxiv. 2025 Mar 10:2025.03.07.642063. doi: 10.1101/2025.03.07.642063.
Changes in RNA splicing over the course of evolution have profoundly diversified the functional landscape of the human genome. While DNA sequences proximal to intron-exon junctions are known to be critical for RNA splicing, the impact of distal intronic sequences remains underexplored. Emerging evidence suggests that inverted pairs of intronic Alu elements can promote exon skipping by forming RNA stem-loop structures. However, their prevalence and influence throughout evolution remain unknown.
Here, we present a systematic analysis of inverted Alu pairs across the human genome to assess their impact on exon skipping through predicted RNA stem-loop formation and their relevance to hominoid evolution. We found that inverted Alu pairs, particularly pairs of AluY-AluSx1 and AluSz-AluSx, are enriched in the flanking regions of skippable exons genome-wide and are predicted to form stable stem-loop structures. Exons defined by weak 3' acceptor and strong 5' donor splice sites appear especially prone to this skipping mechanism. Through comparative genome analysis across nine primate species, we identified 67,126 hominoid-specific Alu insertions, primarily from AluY and AluS subfamilies, which form inverted pairs enriched across skippable exons in genes of ubiquitination-related pathways. Experimental validation of exon skipping among several hominoid-specific inverted Alu pairs further reinforced their potential evolutionary significance.
This work extends our current knowledge of the roles of RNA secondary structure formed by inverted Alu pairs and details a newly emerging mechanism through which transposable elements have contributed to genomic innovation across hominoid evolution at the transcriptomic level.
在进化过程中，RNA剪接的变化使人类基因组的功能格局发生了深刻的多样化。虽然已知内含子-外显子连接处附近的DNA序列对RNA剪接至关重要，但远端内含子序列的影响仍未得到充分探索。新出现的证据表明，内含子Alu元件的反向配对可以通过形成RNA茎环结构来促进外显子跳跃。然而，它们在整个进化过程中的普遍性和影响仍然未知。
在这里，我们对整个人类基因组中的反向Alu配对进行了系统分析，以评估它们通过预测的RNA茎环形成对外显子跳跃的影响以及它们与类人猿进化的相关性。我们发现，反向Alu配对，特别是AluY-AluSx1和AluSz-AluSx配对，在全基因组可跳跃外显子的侧翼区域富集，并预计会形成稳定的茎环结构。由弱3'受体和强5'供体剪接位点定义的外显子似乎特别容易受到这种跳跃机制的影响。通过对九个灵长类物种的比较基因组分析，我们鉴定出67126个类人猿特异性Alu插入，主要来自AluY和AluS亚家族，它们形成了在泛素化相关途径基因的可跳跃外显子中富集的反向配对。对几个类人猿特异性反向Alu配对中外显子跳跃的实验验证进一步强化了它们潜在的进化意义。
这项工作扩展了我们目前对反向Alu配对形成的RNA二级结构作用的认识，并详细阐述了一种新出现的机制，通过该机制转座元件在转录组水平上对类人猿进化过程中的基因组创新做出了贡献。
