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

Shao, Wei, Zhao, Qiong-Yi, Wang, Xiu-Ye, Xu, Xin-Yan, Tang, Qing, Li, Muwang, Li, Xuan and Xu, Yong-Zhen (2012) Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome. RNA, 18 7: 1395-1407. doi:10.1261/rna.029751.111

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Author Shao, Wei
Zhao, Qiong-Yi
Wang, Xiu-Ye
Xu, Xin-Yan
Tang, Qing
Li, Muwang
Li, Xuan
Xu, Yong-Zhen
Title Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome
Formatted title
Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome 
Journal name RNA   Check publisher's open access policy
ISSN 1355-8382
1469-9001
Publication date 2012-01-01
Sub-type Article (original research)
DOI 10.1261/rna.029751.111
Open Access Status File (Publisher version)
Volume 18
Issue 7
Start page 1395
End page 1407
Total pages 13
Place of publication Woodbury, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Language eng
Abstract 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. Published by Cold Spring Harbor Laboratory Press. Copyright
Keyword Alternative splicing
Bombyx mori
RNA-seq
SR protein
Trans-splicing
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Brain Institute Publications
 
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Citation counts: TR Web of Science Citation Count  Cited 13 times in Thomson Reuters Web of Science Article | Citations
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