Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome
Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome
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DOI：
10.1261/rna.029751.111
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发表时间：
2012-07-01
期刊：
影响因子：
4.5
通讯作者：
Xu, Yong-Zhen
中科院分区：
文献类型：
--
作者：
Shao, Wei;Zhao, Qiong-Yi;Xu, Yong-Zhen
家蚕的选择性剪接和反式剪接事件尚未得到系统的研究。在此，通过RNA-seq分析家蚕转录组。我们鉴定了320个新基因，修改了1140个基因模型，发现了数千个选择性剪接和58个反式剪接事件。对三种SR蛋白的研究表明，它们的选择性剪接模式和mRNA产物从昆虫到人类都是保守的，并且具有保留内含子的Srsf 6的一种异构体在家蚕性腺中具有性别特异性表达。实验证实了家蚕中mod（mdg 4）的反式剪接。我们鉴定了来自一个共同的5 '-基因的整合，该基因具有46个新鉴定的位于两条DNA链上超过500 kb区域的替代3'-外显子。B中的其他反式剪接事件。其中12个事件被RT-PCR证实，6个事件被嵌合SNPs进一步证实，2个事件被等位基因特异性RT-PCR证实，表明反式剪接在昆虫中比以前认为的更普遍。分析了B。通过RNA-seq技术对mori转录组进行分析，为研究选择性剪接事件的调控机制提供了有价值的信息。跨物种剪接事件的保守性和新鉴定的反式剪接事件表明B.森是今后研究的良好模式。
Alternative splicing and trans-splicing events have not been systematically studied in the silkworm Bombyx mori. Here, the silkworm transcriptome was analyzed by RNA-seq. We identified 320 novel genes, modified 1140 gene models, and found thousands of alternative splicing and 58 trans-splicing events. Studies of three SR proteins show that both their alternative splicing patterns and mRNA products are conserved from insect to human, and one isoform of Srsf6 with a retained intron is expressed sex-specifically in silkworm gonads. Trans-splicing of mod(mdg4) in silkworm was experimentally confirmed. We identified integrations from a common 5'-gene with 46 newly identified alternative 3'-exons that are located on both DNA strands over a 500-kb region. Other trans-splicing events in B. mori were predicted by bioinformatic analysis, in which 12 events were confirmed by RT-PCR, six events were further validated by chimeric SNPs, and two events were confirmed by allele-specific RT-PCR in F-1 hybrids from distinct silkworm lines of JS and L10, indicating that trans-splicing is more widespread in insects than previously thought. Analysis of the B. mori transcriptome by RNA-seq provides valuable information of regulatory alternative splicing events. The conservation of splicing events across species and newly identified trans-splicing events suggest that B. mori is a good model for future studies.