RT Journal
A1 Fu, Haihui
A1 Yang, Dewei
A1 Su, Wenyue
A1 Ma, Liuyin
A1 Shen, Yingjia
A1 Ji, Guoli
A1 Ye, Xinfu
A1 Wu, Xiaohui
A1 Li, Qingshun Q.
T1 Genome-wide dynamics of alternative polyadenylation in rice
JF Genome Research 
JO Genome Research 
YR 2016 
FD December 01 
VO 26 
IS 12 
SP 1753 
OP 1760 
DO 10.1101/gr.210757.116 
UL http://genome.cshlp.org/content/26/12/1753.abstract 
AB 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.