Genome-wide dynamics of alternative polyadenylation in rice
- Haihui Fu1,
- Dewei Yang2,
- Wenyue Su1,
- Liuyin Ma1,
- Yingjia Shen1,
- Guoli Ji1,
- Xingfu Ye2,
- Xiaohui Wu1 and
- Qingshun Quinn Li3,4
- ↵* Corresponding author; email: qqli{at}westernu.edu
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' UTR. Interestingly, APA in mature pollen are distinct where differential expression level of a set of poly(A) factors and different distribution of APA sites were 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 are associated with trait formation in eukaryotes.
- Received May 31, 2016.
- Accepted October 6, 2016.
- Published by Cold Spring Harbor Laboratory Press
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