Published online 27 September 2004
Nucleic Acids Research, Vol. 32 No. 17 © Oxford University Press 2004; all rights reserved
Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences
1 Plant Mutation Exploration Team, Plant Functional Genomics Research Group and 2 Genomic Knowledge Base Research Team, Bioinformatics Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan and 3 Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba 305-0074, Japan
* To whom correspondence should be addressed. Tel: +81 29 836 4359; Fax: +81 29 836 9060; Email: sinozaki{at}rtc.riken.jp
Present address: Kei Iida, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
Received July 14, 2004; Revised and Accepted September 6, 2004
We mapped RIKEN Arabidopsis full-length (RAFL) cDNAs to the Arabidopsis thaliana genome to search for alternative splicing events. We used 278 734 full-length and 3'/5' terminal reads of the sequences of 220 214 RAFL cDNA clones for the analysis. Eighty-nine percent of the cDNA sequences could be mapped to the genome and were clustered in 17 130 transcription units (TUs). Alternative splicing events were found in 1764 out of 15 214 TUs (11.6%) with multiple sequences. We collected full-length cDNA clones from plants grown under various environmental conditions or from various organs. We then analyzed the correlation between alternative splicing events and environmental stress conditions. Alternative splicing profiles changed according to environmental stress conditions and the various developmental stages of plant organs. In particular, cold-stress conditions affected alternative splicing profiles. The change in alternative splicing profiles under cold stress may be mediated by alternative splicing and transcriptional regulation of splicing factors.
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