Intronic antisense Alu elements have a negative splicing effect on the inclusion of adjacent downstream exons
Intronic antisense Alu elements have a negative splicing effect on the inclusion of adjacent downstream exons
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DOI：
10.1016/j.gene.2018.04.064
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发表时间：
2018-07-20
期刊：
影响因子：
3.5
通讯作者：
Fukao, Toshiyuki
中科院分区：
文献类型：
--
作者：
Nakama, Mina;Otsuka, Hiroki;Fukao, Toshiyuki
Alu元件占人类基因组的10%。然而，尽管它们有助于基因组和转录组多样性，但它们的功能仍然没有完全理解。我们假设内含子Alu元件可能有助于选择性剪接。因此，我们使用包括外显子9-外显子11（包括具有截短内含子9和10的ACAT 1）的小基因构建体研究了它们对剪接的影响。这些构建体含有内含子9的次优剪接受体位点。插入AIuY-部分的AITSz 6-AITSx，最初位于ACAT 1内含子5，在内含子9内的反义方向有负面影响外显子10的列入。这种效应与外显子10中的外显子剪接增强子突变的效应是相加的，并且通过将外显子10的第一个核苷酸Cat替换为G而被取消，这优化了内含子9的剪接受体位点。一个有义ALuY-部分ALuSz 6-ALuSx插入对外显子10的包含没有影响，一个反义ALuSx插入与反义ALuY-部分ALuSz 6-ALuSx插入具有相似的效果。反义Alu元件与外显子10之间的距离越短，对外显子10包含的负面影响越大。这种距离效应对于次优剪接位点比最优剪接位点更明显。基于我们的数据，我们提出，内含子反义Alu元件有助于选择性剪接和转录组的多样性在某些基因，特别是当剪接受体位点是次优的。
Alu elements occupy 10% of the human genome. However, although they contribute to genomic and transcriptomic diversity, their function is still not fully understood. We hypothesized that intronic Alu elements may contribute to alternative splicing. We therefore examined their effect on splicing using minigene constructs including exon 9-exon 11 inclusive of ACAT1 with truncated introns 9 and 10. These constructs contained a suboptimal splice acceptor site for intron 9. Insertion of AIuY-partial AluSz6-AluSx, originally located in ACAT1 intron 5, in an antisense direction within intron 9 had a negative effect on exon 10 inclusion. This effect was additive with that of an exonic splicing enhancer mutation in exon 10, and was canceled by the substitution of G for Cat the first nucleotide of exon 10 which optimized the splice acceptor site of intron 9. A sense ALuY-partial AluSz6-AluSx insertion had no effect on exon 10 inclusion, and one antisense AluSx insertion had a similar effect to antisense AluY-partial AluSz6-AluSx insertion. The shorter the distance between the antisense Alu element and exon 10, the greater the negative effect on exon 10 inclusion. This distance effect was more evident for suboptimal than optimal splice sites. Based on our data, we propose that intronic antisense Alu elements contribute to alternative splicing and transcriptomic diversity in some genes, especially when splice acceptor sites are suboptimal.