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Bioinformatics Advance Access published online on January 12, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti253
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Bioinformatics © Oxford University Press 2005; all rights reserved.
Received September 2, 2004
Revised December 17, 2004
Accepted December 27, 2004

Article

Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa)

Noriyuki Kitagawa 1, Takanori Washio 2*, Shunichi Kosugi 3, Tomoya Yamashita 1, Kenji Higashi 1, Hiroshi Yanagawa 3, Kenichi Higo 4, Koji Satoh 4, Yasuhiro Ohtomo 5, Tomomi Sunako 5, Kazuo Murakami 5, Kenichi Matsubara 5, Jun Kawai 6, Piero Carninci 6, Yoshihide Hayashizaki 6, Shoshi Kikuchi 4, and Masaru Tomita 7

1 Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan; Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan
2 Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan; Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
3 Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
4 National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
5 Foundation for Advancement of International Science (FAIS), Tsukuba, Ibaraki 305-0062, Japan
6 Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
7 Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan; Department of Environmental Information, Keio University, Fujisawa, Kanagawa 252-8520, Japan

* To whom correspondence should be addressed.
Takanori Washio, E-mail: washy{at}sfc.keio.ac.jp


  Abstract

Motivation: Transcription start site selection and alternative splicing greatly contribute to diversifying gene expression. Recent studies have revealed the existence of alternative first exons, but most have involved mammalian genes, and as yet the regulation of usage of alternative first exons has not been clarified, especially in plants.

Results and Discussion: We systematically identified putative alternative first exon transcripts in rice, verified the candidates using reverse transcription-polymerase chain reaction (RT-PCR), and searched for the promoter elements that might regulate the alternative first exons. As a result, we detected a number of unreported alternative first exons, some of which are regulated in a tissue-specific manner.

Supplementary Information: Supplementary materials can be accessed.


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