Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation

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	Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation
	Shen, Yingjia ; Ji, Guoli ; Haas, Brian J. ; Wu, Xiaohui ; Zheng, Jianti ; Reese, Greg J. ; Li, Qingshun Quinn ; Ji GL(吉国力)
刊名	http://dx.doi.org/10.1093/nar/gkn158
	2008-05
关键词	EXPRESSION ANALYSIS UPSTREAM ELEMENT POINT MUTATIONS ARABIDOPSIS SITES MECHANISM CLEAVAGE AAUAAA PLANTS GENES
英文摘要	The position of a poly(A) site of eukaryotic mRNA is determined by sequence signals in pre-mRNA and a group of polyadenylation factors. To reveal rice poly(A) signals at a genome level, we constructed a dataset of 55 742 authenticated poly(A) sites and characterized the poly(A) signals. This resulted in identifying the typical tripartite cis-elements, including FUE, NUE and CE, as previously observed in Arabidopsis. The average size of the 3'-UTR was 289 nucleotides. When mapped to the genome, however, 15% of these poly(A) sites were found to be located in the currently annotated intergenic regions. Moreover, an extensive alternative polyadenylation profile was evident where 50% of the genes analyzed had more than one unique poly(A) site (excluding microheterogeneity sites), and 13% had four or more poly(A) sites. About 4% of the analyzed genes possessed alternative poly(A) sites at their introns, 5'-UTRs, or protein coding regions. The authenticity of these alternative poly(A) sites was partially confirmed using MPSS data. Analysis of nucleotide profile and signal patterns indicated that there may be a different set of poly(A) signals for those poly(A) sites found in the coding regions. Based on the features of rice poly(A) signals, an updated algorithm termed PASS-Rice was designed to predict poly(A) sites.
语种	英语
内容类型	期刊论文
源URL	[http://dspace.xmu.edu.cn/handle/2288/70695]
专题	信息技术－已发表论文
推荐引用方式 GB/T 7714	Shen, Yingjia,Ji, Guoli,Haas, Brian J.,et al. Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation[J]. http://dx.doi.org/10.1093/nar/gkn158,2008.
APA	Shen, Yingjia.,Ji, Guoli.,Haas, Brian J..,Wu, Xiaohui.,Zheng, Jianti.,...&吉国力.(2008).Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation.http://dx.doi.org/10.1093/nar/gkn158.
MLA	Shen, Yingjia,et al."Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation".http://dx.doi.org/10.1093/nar/gkn158 (2008).