Short Homologous Sequences Are Strongly Associated with the Generation of Chimeric RNAs in Eukaryotes
Short Homologous Sequences Are Strongly Associated with the Generation of Chimeric RNAs in Eukaryotes
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DOI：
10.1007/s00239-008-9187-0
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发表时间：
2009-01-01
影响因子：
3.9
通讯作者：
Wang, Wen
中科院分区：
文献类型：
--
作者：
Li, Xin;Zhao, Li;Wang, Wen
嵌合RNA已在多种生物体中报道，并且通常认为是通过两种或更多种不同转录物的反式剪接产生的。在这里，我们在芽殖酵母、果蝇、小鼠和人类中进行了大规模的嵌合RNA搜索。在这些生物体中发现了数千种嵌合转录物，但在酵母中发现了5种嵌合RNA。使用特异性引物对酵母和苍蝇嵌合转录物样品进行的RT-PCR实验表明，这些嵌合RNA中约有三分之一可以复制。这些结果表明，至少相当数量的嵌合RNA不太可能来自异常转录或剪接，因此嵌合RNA的形成可能是一个广泛的过程，并且可以极大地促进生物体的转录组和蛋白质组的复杂性。然而，这些嵌合RNA中只有一小部分（< 20%）在接合序列处具有GU-AG，这符合经典的反式剪接模型。相反，我们观察到约一半的嵌合RNA在源序列的连接位点处具有短同源序列（SHS）。我们在酵母中的序列突变实验表明，SHS的破坏导致相应的嵌合RNA的消失，这表明SHS是产生这种嵌合RNA所必需的。除了经典的反式剪接模型，我们提出了一个新的模型，转录滑移模型，来解释这些嵌合RNA的产生与SHS模板合成。
Chimeric RNAs have been reported in varieties of organisms and are conventionally thought to be produced by trans-splicing of two or more distinct transcripts. Here, we conducted a large-scale search for chimeric RNAs in the budding yeast, fruit fly, mouse, and human. Thousands of chimeric transcripts were identified in these organisms except in yeast, in which five chimeric RNAs were observed. RT-PCR experiments for a sample of yeast and fly chimeric transcripts using specific primers show that about one-third of these chimeric RNAs can be reproduced. The results suggest that at least a considerable amount of chimeric RNAs is unlikely from aberrant transcription or splicing, and thus formation of chimeric RNAs is probably a widespread process and can greatly contribute to the complexity of the transcriptome and proteome of organisms. However, only a small fraction (< 20%) of these chimeric RNAs has GU-AG at the junction sequences which fits the classical trans-splicing model. In contrast, we observed that about half of the chimeric RNAs have short homologous sequences (SHSs) at the junction sites of the source sequences. Our sequence mutation experiments in yeast showed that disruption of SHSs resulted in the disappearance of the corresponding chimeric RNAs, suggesting that SHSs are essential for generating this kind of chimeric RNA. In addition to the classical trans-splicing model, we propose a new model, the transcriptional slippage model, to explain the generation of those chimeric RNAs synthesized from templates with SHSs.