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

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	Bioinformatics Analysis of Alternative Polyadenylation in Green Alga Chlamydomonas reinhardtii Using Transcriptome Sequences from Three Different Sequencing Platforms
	Zhao, Zhixin ; Wu, Xiaohui ; Kumar, Praveen Kumar Raj ; Dong, Min ; Ji, Guoli ; Li, Qingshun Quinn ; Liang, Chun ; Wu XH(吴小惠) ; Ji GL(吉国力)
刊名	http://dx.doi.org/10.1534/g3.114.010249
	2014-05-01
关键词	MESSENGER-RNA POLYADENYLATION ARABIDOPSIS SIGNALS GENES CDNA WIDESPREAD LANDSCAPE EVOLUTION ELEMENTS CLEAVAGE
英文摘要	NIH AREA [1R15GM94732-1 A1]; National Natural Science Foundation of China [61174161, 61201358]; Natural Science Foundation of Fujian Province of China [2012J01154]; specialized Research Fund for the Doctoral Program of Higher Education of China [20130121130004, 20120121120038]; Fundamental Research Funds for the Central Universities in China (Xiamen University) [2011121047, 201112G018, 201212G005, 2013121025]; Fundamental Research Fund for the university student Creative and Entrepreneurship training program in China (Xiamen University) [XDDC201210384063]; 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.
语种	英语
出版者	GENETICS SOC AM
内容类型	期刊论文
源URL	[http://dspace.xmu.edu.cn/handle/2288/92687]
专题	信息技术－已发表论文
推荐引用方式 GB/T 7714	Zhao, Zhixin,Wu, Xiaohui,Kumar, Praveen Kumar Raj,et al. Bioinformatics Analysis of Alternative Polyadenylation in Green Alga Chlamydomonas reinhardtii Using Transcriptome Sequences from Three Different Sequencing Platforms[J]. http://dx.doi.org/10.1534/g3.114.010249,2014.
APA	Zhao, Zhixin.,Wu, Xiaohui.,Kumar, Praveen Kumar Raj.,Dong, Min.,Ji, Guoli.,...&吉国力.(2014).Bioinformatics Analysis of Alternative Polyadenylation in Green Alga Chlamydomonas reinhardtii Using Transcriptome Sequences from Three Different Sequencing Platforms.http://dx.doi.org/10.1534/g3.114.010249.
MLA	Zhao, Zhixin,et al."Bioinformatics Analysis of Alternative Polyadenylation in Green Alga Chlamydomonas reinhardtii Using Transcriptome Sequences from Three Different Sequencing Platforms".http://dx.doi.org/10.1534/g3.114.010249 (2014).