title: Alternative splicing at NAGNAG acceptor sites shares common properties in land plants and mammals.
abstract: 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.
authors.affiliation: Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan. kiida@ucr.edu
authors.forename: Kei
authors.initials: K
authors.lastname: Iida
authors.forename: Masafumi
authors.initials: M
authors.lastname: Shionyu
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Suso
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D000595:Amino Acid Sequence; D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D017343:Genes, Plant; D016678:Genome; D006801:Humans; D007438:Introns / Q000235:genetics; D008322:Mammals / Q000235:genetics*; D051379:Mice; D008958:Models, Molecular; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics; D010940:Plant Proteins / Q000737:chemistry; D010944:Plants / Q000235:genetics*; D017434:Protein Structure, Tertiary; D022821:RNA Splice Sites / Q000235:genetics*; D016415:Sequence Alignment; D014158:Transcription, Genetic
chemical_list: D010940:Plant Proteins; D022821:RNA Splice Sites