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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Shen, Yingjia Venu, R. C. Nobuta, Kan Wu, Xiaohui Notibala, Varun Demirci, Caghan Meyers, Blake C. Wang, Guo-Liang Ji, Guoli Li, Qingshun Q. |
| Description | Country affiliation: United States Author Affiliation: Shen Y ( Department of Botany, Miami University, Oxford, OH 45056, 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 â¼60% of Arabidopsis genes have multiple poly(A) sites. Likewise, â¼47% and 82% of rice genes use APA, supported by MPSS-DGE and SBS-DGE tags, respectively. In both species, â¼49%-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. |
| File Format | HTM / HTML |
| ISSN | 10889051 |
| e-ISSN | 15495469 |
| DOI | 10.1101/gr.114744.110 |
| Journal | Genome Research |
| Issue Number | 9 |
| Volume Number | 21 |
| Language | English |
| Publisher | Cold Spring Harbor Laboratory Press |
| Publisher Date | 2011-09-01 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Discipline Genetics Discipline Genomics Plants Genetics Polyadenylation Transcriptome Arabidopsis Gene Expression Profiling Gene-environment Interaction Genes, Plant High-throughput Nucleotide Sequencing Organ Specificity Oryza Sativa Rna, Messenger Metabolism Sequence Analysis, Rna Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't Research Support, U.s. Gov't, Non-p.h.s. |
| Content Type | Text |
| Resource Type | Article |
| Subject | Genetics Genetics (clinical) |
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