RT Journal
A1 Shen, Yingjia
A1 Venu, R.C.
A1 Nobuta, Kan
A1 Wu, Xiaohui
A1 Notibala, Varun
A1 Demirci, Caghan
A1 Meyers, Blake C.
A1 Wang, Guo-Liang
A1 Ji, Guoli
A1 Li, Qingshun Q.
T1 Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing
JF Genome Research 
JO Genome Research 
YR 2011 
FD September 01 
VO 21 
IS 9 
SP 1478 
OP 1486 
DO 10.1101/gr.114744.110 
UL http://genome.cshlp.org/content/21/9/1478.abstract 
AB Polyadenylation sites mark the ends of mRNA transcripts. Alternative polyadenylation (APA) may alter sequence elements and/or the coding capacity of transcripts, a mechanism that has been demonstrated to regulate gene expression and transcriptome diversity. To study the role of APA in transcriptome dynamics, we analyzed a large-scale data set of RNA “tags” that signify poly(A) sites and expression levels of mRNA. These tags were derived from a wide range of tissues and developmental stages that were mutated or exposed to environmental treatments, and generated using digital gene expression (DGE)–based protocols of the massively parallel signature sequencing (MPSS-DGE) and the Illumina sequencing-by-synthesis (SBS-DGE) sequencing platforms. The data offer a global view of APA and how it contributes to transcriptome dynamics. Upon analysis of these data, we found that ∼60% of Arabidopsis genes have multiple poly(A) sites. Likewise, ∼47% and 82% of rice genes use APA, supported by MPSS-DGE and SBS-DGE tags, respectively. In both species, ∼49%–66% of APA events were mapped upstream of annotated stop codons. Interestingly, 10% of the transcriptomes are made up of APA transcripts that are differentially distributed among developmental stages and in tissues responding to environmental stresses, providing an additional level of transcriptome dynamics. Examples of pollen-specific APA switching and salicylic acid treatment-specific APA clearly demonstrated such dynamics. The significance of these APAs is more evident in the 3034 genes that have conserved APA events between rice and Arabidopsis.