Genome-wide dynamics of alternative polyadenylation in rice

Haihui Fu; Dewei Yang; Wenyue Su; Liuyin Ma; Yingjia Shen; Guoli Ji; Xinfu Ye; Xiaohui Wu; Qingshun Q. Li

doi:10.1101/gr.210757.116

Genome-wide dynamics of alternative polyadenylation in rice

¹Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China, 361102;
²Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China, 350018;
³Department of Automation, Xiamen University, Xiamen, Fujian, China, 361005;
⁴Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California 91766, USA

Corresponding authors: xhuister{at}xmu.edu.cn, yexinfu{at}126.com, qqli{at}westernu.edu

↵5 These authors contributed equally to this work.

Abstract

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.

Footnotes

[Supplemental material is available for this article.]
Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.210757.116.

Received May 31, 2016.
Accepted October 6, 2016.

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