MBE Advance Access originally published online on January 29, 2008
Molecular Biology and Evolution 2008 25(4):709-718; doi:10.1093/molbev/msn015
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Research Articles |
Alternative Splicing at NAGNAG Acceptor Sites Shares Common Properties in Land Plants and Mammals
Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
E-mail: kiida{at}ucr.edu.
Accepted for publication January 9, 2008.
In recent years, several papers have reported that a special type of alternative splicing (AS) event occurs at the tandem 3' splice site, termed the "NAGNAG acceptor." This type of AS event (termed AS-NAGNAG) is well studied in both human and mouse. To illustrate the significance of AS-NAGNAG events, we focused on their occurrence in Arabidopsis thaliana and Oryza sativa (rice). Our study is the first genome-wide approach examining AS-NAGNAG events in land plants. Based on transcripts and genomic sequences, we found 321 and 372 AS-NAGNAG events in Arabidopsis and rice, respectively. These events were significantly enriched in genes encoding DNA-binding proteins, and more than half of all AS-NAGNAG events affected polar amino acid residues. The observed properties of AS-NAGNAG events in plants were similar to those seen in mammals. These results showed that AS-NAGNAG events may provide a mechanism for fine-tuning of DNA-binding proteins in both mammals and land plants. We found 7 gene groups of AS-NAGNAG events that were conserved between Arabidopsis and rice, including 2 groups for RNA-binding proteins. Conservation of the events for RNA-binding proteins is a property also seen in mammals. Furthermore, we found 23 gene groups containing AS-NAGNAG events that occurred in noncorresponding introns of homologous genes. They included 5 groups of DNA-binding proteins, whose number was larger than expected. We think there is a bias with which AS-NAGNAG events are fixed in genes for DNA-binding proteins. Our analysis showed that AS-NAGNAG events found in land plants share similar properties with those in mammals. Based on our results, we propose that AS-NAGNAG events are likely to be a common mechanism in the fine-tuning of protein functions, especially DNA/RNA-binding proteins, in both mammals and plants. Their role might contribute to the construction of complicated transcriptomes and proteomes in the evolutionary history of mammals and land plants.
Key Words: Arabidopsis thaliana • Oryza sativa • NAGNAG acceptor • alternative splicing • evolution of transcriptome
1 Present address: Department of Botany and Plant Sciences, University of California, Riverside.