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Bioinformatics Analysis of Alternative Polyadenylation in Green Alga Chlamydomonas reinhardtii Using Transcriptome Sequences from Three Different Sequencing Platforms

文献类型： 外文期刊

作者： Zhao, Zhixin 1 ; Wu, Xiaohui 1 ; Kumar, Praveen Kumar Raj 1 ; Dong, Min 1 ; Ji, Guoli 2 ; Li, Qingshun Quinn 1 ; Liang 1 ;

作者机构： 1.Miami Univ, Dept Biol, Oxford, OH 45056 USA

2.Xiamen Univ, Dept Automat, Xiamen 361005, Peoples R China

3.Xiamen Univ, Minist Educ Coastal & Wetland Ecosyst, Key Lab, Xiamen 361102, Fujian, Peoples R China

4.Xiamen Univ, Coll Environm & Ecol, Xiamen 361102, Fujian, Peoples R China

5.Fujian Acad Agr Sci, Rice Res Inst, Fuzhou 350003, Fujian, Peoples R China

关键词： poly(A) signals;alternative polyadenylation;alternative splicing;intron retention;sequencing platforms;Chlamydomonas reinhardtii

期刊名称：G3-GENES GENOMES GENETICS （ 影响因子：3.154； 五年影响因子：3.369 ）

ISSN： 2160-1836

年卷期： 2014 年 4 卷 5 期

页码：

收录情况： SCI

摘要： Messenger RNA 3-end formation is an essential posttranscriptional processing step for most eukaryotic genes. Different from plants and animals where AAUAAA and its variants routinely are found as the main poly(A) signal, Chlamydomonas reinhardtii uses UGUAA as the major poly(A) signal. The advance of sequencing technology provides an enormous amount of sequencing data for us to explore the variations of poly(A) signals, alternative polyadenylation (APA), and its relationship with splicing in this algal species. Through genome-wide analysis of poly(A) sites in C. reinhardtii, we identified a large number of poly(A) sites: 21,041 from Sanger expressed sequence tags, 88,184 from 454, and 195,266 from Illumina sequence reads. In comparison with previous collections, more new poly(A) sites are found in coding sequences and intron and intergenic regions by deep-sequencing. Interestingly, G-rich signals are particularly abundant in intron and intergenic regions. The prevalence of different poly(A) signals between coding sequences and a 3-untranslated region implies potentially different polyadenylation mechanisms. Our data suggest that the APA occurs in about 68% of C. reinhardtii genes. Using Gene Ontolgy analysis, we found most of the APA genes are involved in RNA regulation and metabolic process, protein synthesis, hydrolase, and ligase activities. Moreover, intronic poly(A) sites are more abundant in constitutively spliced introns than retained introns, suggesting an interplay between polyadenylation and splicing. Our results support that APA, as in higher eukaryotes, may play significant roles in increasing transcriptome diversity and gene expression regulation in this algal species. Our datasets also provide useful information for accurate annotation of transcript ends in C. reinhardtii.

  • 相关文献

[1]Genome-wide identification and predictive modeling of polyadenylation sites in eukaryotes. Ji, Guoli,Guan, Jinting,Zeng, Yong,Wu, Xiaohui,Ji, Guoli,Li, Qingshun Q.,Li, Qingshun Q.,Li, Qingshun Q..

[2]Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana. Wu, Xiaohui,Zeng, Yong,Guan, Jinting,Ji, Guoli,Huang, Rongting,Li, Qingshun Q.,Li, Qingshun Q.,Li, Qingshun Q.,Ji, Guoli. 2015

[3]Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. Wu, Xiaohui,Gaffney, Bobby,Hunt, Arthur G.,Li, Qingshun Q.,Li, Qingshun Q.,Li, Qingshun Q.. 2014

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