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Genome-wide dynamics of alternative polyadenylation in rice

文献类型： 外文期刊

作者： Fu, Haihui 1 ; Yang, Dewei 2 ; Su, Wenyue 1 ; Ma, Liuyin 1 ; Shen, Yingjia 1 ; Ji, Guoli 3 ; Ye, Xinfu 2 ; Wu, Xiaohui 3 ; L 1 ;

作者机构： 1.Xiamen Univ, Coll Environm & Ecol, Key Lab, Minist Educ Coastal & Wetland Ecosyst, Xiamen 361102, Fujian, Peoples R China

2.Fujian Acad Agr Sci, Rice Res Inst, Fuzhou 350018, Fujian, Peoples R China

3.Xiamen Univ, Dept Automat, Xiamen 361005, Fujian, Peoples R China

4.Western Univ Hlth Sci, Grad Coll Biomed Sci, Po

期刊名称：GENOME RESEARCH （ 影响因子：9.043； 五年影响因子：12.808 ）

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收录情况： SCI

摘要： Alternative polyadenylation (APA), in which a transcript uses one of the poly(A) sites to define its 3'-end, is a common regulatory mechanism in eukaryotic gene expression. However, the potential of APA in determining crop agronomic traits remains elusive. This study systematically tallied poly(A) sites of 14 different rice tissues and developmental stages using the poly(A) tag sequencing (PAT-seq) approach. The results indicate significant involvement of APA in developmental and quantitative trait loci (QTL) gene expression. About 48% of all expressed genes use APA to generate transcriptomic and proteomic diversity. Some genes switch APA sites, allowing differentially expressed genes to use alternate 3' UTRs. Interestingly, APA in mature pollen is distinct where differential expression levels of a set of poly(A) factors and different distributions of APA sites are found, indicating a unique mRNA 3'-end formation regulation during gametophyte development. Equally interesting, statistical analyses showed that QTL tends to use APA for regulation of gene expression of many agronomic traits, suggesting a potential important role of APA in rice production. These results provide thus far the most comprehensive and high-resolution resource for advanced analysis of APA in crops and shed light on how APA is associated with trait formation in eukaryotes.

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