Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome

被引:46
作者
Shao, Wei [2 ]
Zhao, Qiong-Yi [1 ]
Wang, Xiu-Ye [2 ]
Xu, Xin-Yan [2 ]
Tang, Qing [2 ]
Li, Muwang [3 ]
Li, Xuan [1 ]
Xu, Yong-Zhen [2 ]
机构
[1] Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Plant Physiol & Ecol, Key Lab Synthet Biol, Shanghai 200032, Peoples R China
[2] Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Plant Physiol & Ecol, Key Lab Insect Dev & Evolutionary Biol, Shanghai 200032, Peoples R China
[3] Chinese Acad Agr Sci, Sericultural Res Inst, Zhenjiang 212018, Jiangsu, Peoples R China
关键词
RNA-seq; alternative splicing; trans-splicing; Bombyx mori; SR protein; SILKWORM BOMBYX; REGULATORY ELEMENTS; GENE-EXPRESSION; DROSOPHILA; COMPLEXITY; DOUBLESEX; GENOME; LOCUS; MECHANISMS; MOD(MDG4);
D O I
10.1261/rna.029751.111
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:1395 / 1407
页数:13
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