title: Intron retention is a major phenomenon in alternative splicing in Arabidopsis.
abstract: Alternative splicing (AS) combines different transcript splice junctions that result in transcripts with shuffled exons, alternative 5' or 3' splicing sites, retained introns and different transcript termini. In this way, multiple mRNA species and proteins can be created from a single gene expanding the potential informational content of eukaryotic genomes. Search algorithms of AS forms in a variety of Arabidopsis databases showed they contained an unusually high fraction of retained introns (above 30%), compared with 10% that was reported for humans. The preponderance of retained introns (65%) were either part of open reading frames, present in the UTR region or present as the last intron in the transcript, indicating that their occurrence would not participate in non-sense-mediated decay. Interestingly, the functional distribution of the transcripts with retained introns is skewed towards stress and external/internal stimuli-related functions. A sampling of the alternative transcripts with retained introns were confirmed by RT-PCR and were shown to co-purify with polyribosomes, indicating their nuclear export. Thus, retained introns are a prominent feature of AS in Arabidopsis and as such may play a regulatory function.
authors.affiliation: Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Hadas
authors.initials: H
authors.lastname: Ner-Gaon
authors.forename: Ronit
authors.initials: R
authors.lastname: Halachmi
authors.forename: Sigal
authors.initials: S
authors.lastname: Savaldi-Goldstein
authors.forename: Eitan
authors.initials: E
authors.lastname: Rubin
authors.forename: Ron
authors.initials: R
authors.lastname: Ophir
authors.forename: Robert
authors.initials: R
authors.lastname: Fluhr
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D017360:Arabidopsis / Q000235:genetics*; D020224:Expressed Sequence Tags; D007438:Introns / Q000235:genetics*; D011132:Polyribosomes / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D018749:RNA, Plant