Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing
- Yingjia Shen1,6,
- R.C. Venu2,
- Kan Nobuta3,
- Xiaohui Wu1,4,
- Varun Notibala3,
- Caghan Demirci3,
- Blake C. Meyers3,5,
- Guo-Liang Wang2,
- Guoli Ji4 and
- Qingshun Q. Li1,7
- 1Department of Botany, Miami University, Oxford, Ohio 45056, USA;
- 2Department of Plant Pathology, Ohio State University, Columbus, Ohio 43210, USA;
- 3Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA;
- 4Department of Automation, Xiamen University, Xiamen 361005, China;
- 5Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711, USA
Abstract
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.
Footnotes
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↵7 Corresponding author.
E-mail liq{at}muohio.edu.
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.114744.110.
- Received September 7, 2010.
- Accepted July 5, 2011.
- Copyright © 2011 by Cold Spring Harbor Laboratory Press
