Department of Botany, Miami University, Oxford, OH 45056, USA
Genome Res. 2011 Sep;21(9):1478-86. doi: 10.1101/gr.114744.110. Epub 2011 Aug 3.
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.
多聚腺苷酸化位点标记 mRNA 转录本的末端。可变多聚腺苷酸化（APA）可能改变序列元件和/或转录本的编码能力，这种机制已被证明可调节基因表达和转录组多样性。为了研究 APA 在转录组动态中的作用，我们分析了一个大规模的 RNA“标签”数据集，这些标签表示多(A) 位点和 mRNA 的表达水平。这些标签源自广泛的组织和发育阶段，这些组织和发育阶段发生了突变或暴露于环境处理中，并且使用数字基因表达（DGE）为基础的大规模平行签名测序（MPSS-DGE）和 Illumina 测序合成（SBS-DGE）测序平台生成。这些数据提供了 APA 的全局视图及其对转录组动态的贡献。在分析这些数据时，我们发现约 60%的拟南芥基因具有多个多聚腺苷酸化位点。同样，约 47%和 82%的水稻基因使用 APA，这分别得到了 MPSS-DGE 和 SBS-DGE 标签的支持。在这两个物种中，约 49%-66%的 APA 事件位于注释的终止密码子上游。有趣的是，10%的转录组由 APA 转录本组成，这些转录本在发育阶段和对环境应激反应的组织中差异分布，提供了转录组动态的额外水平。花粉特异性 APA 转换和水杨酸处理特异性 APA 的例子清楚地证明了这种动态。在水稻和拟南芥之间具有保守 APA 事件的 3034 个基因中，这些 APAs 的意义更为明显。
