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DNA Research Advance Access originally published online on May 7, 2009
DNA Research 2009 16(3):155-164; doi:10.1093/dnares/dsp009
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© The Author 2009. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Analysis of Multiple Occurrences of Alternative Splicing Events in Arabidopsis thaliana Using Novel Sequenced Full-Length cDNAs

Kei Iida1 {dagger}, Kaoru Fukami-Kobayashi2, Atsushi Toyoda3 {ddagger}, Yoshiyuki Sakaki3 ¶, Masatomo Kobayashi2, Motoaki Seki4,* and Kazuo Shinozaki5,*

1 Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
2 RIKEN BioResource Center, RIKEN Tsukuba Institute, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan
3 Sequence Technology Team, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
4 Plant Genomic Network Research Team, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
5 Gene Discovery Research Team, RIKEN Plant Science Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan

Received 11 December 2008 ; accepted 17 April 2009.

Alternative splicing (AS) is a mechanism by which multiple types of mature mRNAs are generated from a single pre-mature mRNA. In this study, we completely sequenced 1800 full-length cDNAs from Arabidopsis thaliana, which had 5' and/or 3' sequences that were previously found to have AS events or alternative transcription start sites. Unexpectedly, these sequences gave us further evidence of AS, as 601 out of 1800 transcripts showed novel AS events. We focused on the combination patterns of multiple AS events within individual genes. Interestingly, some specific AS event combination patterns tended to appear more frequently than expected. The two most common patterns were: (i) alternative donor–0~12 times of exon skips–alternative acceptor and (ii) several times (~8) of retained introns. We also found that multiple AS events in a transcript tend to have the same effects concerning the length of the mature mRNA. Our current results are consistent with our previous observations, which showed changes in AS profiles under different conditions, and suggest the involvement of hypothetical cis- and trans-acting factors in the regulation of AS events.

Key words: Arabidopsis; alternative splicing; bioinformatics; full-length cDNA

* To whom correspondence should be addressed. Tel. +81 29-836-4359. Fax. +81 29-836-9060. E-mail: sinozaki{at}rtc.riken.jp (K.S.); Tel. +81 45-503-9587. Fax. +81 45-503-9584. E-mail: mseki{at}psc.riken.jp (M.S.)

{dagger} Present address: Bioinformatics and Systems Engineering Division, RIKEN Yokohama Institute, 1-7-22, Suehiro, Tsurumi, Yokohama 230-0045, Japan.

{ddagger} Present address: Comparative Genomics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan.

Present address: Toyohashi University of Technology, 1-1, Hibarigaoka, Tenpaku-cho, Toyohashi, Aichi 441-8580, Japan.


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