Single-Nucleotide Resolution Mapping of the Gossypium raimondii   Transcriptome Reveals a New Mechanism for Alternative Splicing of   Introns

doi:10.1093/mp/sst175

CORC > 北京大学 > 生命科学学院

	Single-Nucleotide Resolution Mapping of the Gossypium raimondii Transcriptome Reveals a New Mechanism for Alternative Splicing of Introns
	Li, Qin ; Xiao, Guanghui ; Zhu, Yu-Xian
刊名	分子植物
	2014
关键词	cotton RNA-seq alternative splicing transposable element intron retention COTTON FIBER MESSENGER-RNA ARABIDOPSIS-THALIANA GENOME COMPLEXITY CELL ELONGATION PLANTS GENE RETROTRANSPOSONS MUTATIONS SEQUENCE
DOI	10.1093/mp/sst175
英文摘要	Alternative splicing (AS) is a vital genetic mechanism that enhances the diversity of eukaryotic transcriptomes. Here, we generated 8.3 Gb high-quality RNA-sequencing data from cotton (Gossypium raimondii) and performed a systematic, comparative analysis of AS events. We mapped 85% of the RNA-sequencing data onto the reference genome and identified 154368 splice junctions with 16437 as events in 10197 genes. Intron retention constituted the majority (40%) of all AS events in G. raimondii. Comparison across 11 eukaryote species showed that intron retention is the most common AS type in higher plants. Although transposable elements (TEs) were found in only 2.9% of all G. raimondii introns, they are present in 43% of the retained introns, suggesting that TE-insertion may be an important mechanism for intron retention during AS. The majority of the TE insertions are concentrated 0-40 nt upstream of the 3'-splice site, substantially altering the distribution of branch points from preferred positions and reducing the efficiency of intron splicing by decreasing RNA secondary structure flexibility. Our data suggest that TE-insertion-induced changes in branch point-site distribution are important for intron retention-type AS. Our findings may help explain the vast differences in intron-retention frequencies between vertebrates and higher plants.; Biochemistry & Molecular Biology; Plant Sciences; SCI(E); PubMed; 中国科技核心期刊(ISTIC); 中国科学引文数据库(CSCD); 5; ARTICLE; zhuyx2@pku.edu.cn; 5,SI; 829-840; 7
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/162454]
专题	生命科学学院
推荐引用方式 GB/T 7714	Li, Qin,Xiao, Guanghui,Zhu, Yu-Xian. Single-Nucleotide Resolution Mapping of the Gossypium raimondii Transcriptome Reveals a New Mechanism for Alternative Splicing of Introns[J]. 分子植物,2014.
APA	Li, Qin,Xiao, Guanghui,&Zhu, Yu-Xian.(2014).Single-Nucleotide Resolution Mapping of the Gossypium raimondii Transcriptome Reveals a New Mechanism for Alternative Splicing of Introns.分子植物.
MLA	Li, Qin,et al."Single-Nucleotide Resolution Mapping of the Gossypium raimondii Transcriptome Reveals a New Mechanism for Alternative Splicing of Introns".分子植物 (2014).