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

Noriyuki Kitagawa; Takanori Washio; Shunichi Kosugi; Tomoya Yamashita; Kenji Higashi; Hiroshi Yanagawa; Kenichi Higo; Koji Satoh; Yasuhiro Ohtomo; Tomomi Sunako; Kazuo Murakami; Kenichi Matsubara; Jun Kawai; Piero Carninci; Yoshihide Hayashizaki; Shoshi Kikuchi; Masaru Tomita

doi:10.1093/bioinformatics/bti253

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

Noriyuki Kitagawa, Takanori Washio, Shunichi Kosugi, Tomoya Yamashita, Kenji Higashi, Hiroshi Yanagawa, Kenichi Higo, Koji Satoh, Yasuhiro Ohtomo, Tomomi Sunako, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi, Masaru Tomita

Faculty of Environment and Information Studies

Research output: Contribution to journal › Article › peer-review

23 Citations (Scopus)

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: We systematically identified putative alternative first exon transcripts in rice, verified the candidates using 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.

Original language	English
Pages (from-to)	1758-1763
Number of pages	6
Journal	Bioinformatics
Volume	21
Issue number	9
DOIs	https://doi.org/10.1093/bioinformatics/bti253
Publication status	Published - 2005 May 1

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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Kitagawa, N., Washio, T., Kosugi, S., Yamashita, T., Higashi, K., Yanagawa, H., Higo, K., Satoh, K., Ohtomo, Y., Sunako, T., Murakami, K., Matsubara, K., Kawai, J., Carninci, P., Hayashizaki, Y., Kikuchi, S., & Tomita, M. (2005). Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). Bioinformatics, 21(9), 1758-1763. https://doi.org/10.1093/bioinformatics/bti253

Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). / Kitagawa, Noriyuki; Washio, Takanori; Kosugi, Shunichi; Yamashita, Tomoya; Higashi, Kenji; Yanagawa, Hiroshi; Higo, Kenichi; Satoh, Koji; Ohtomo, Yasuhiro; Sunako, Tomomi; Murakami, Kazuo; Matsubara, Kenichi; Kawai, Jun; Carninci, Piero; Hayashizaki, Yoshihide; Kikuchi, Shoshi; Tomita, Masaru.

In: Bioinformatics, Vol. 21, No. 9, 01.05.2005, p. 1758-1763.

Research output: Contribution to journal › Article › peer-review

Kitagawa, N, Washio, T, Kosugi, S, Yamashita, T, Higashi, K, Yanagawa, H, Higo, K, Satoh, K, Ohtomo, Y, Sunako, T, Murakami, K, Matsubara, K, Kawai, J, Carninci, P, Hayashizaki, Y, Kikuchi, S & Tomita, M 2005, 'Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa)', Bioinformatics, vol. 21, no. 9, pp. 1758-1763. https://doi.org/10.1093/bioinformatics/bti253

Kitagawa, Noriyuki ; Washio, Takanori ; Kosugi, Shunichi ; Yamashita, Tomoya ; Higashi, Kenji ; Yanagawa, Hiroshi ; Higo, Kenichi ; Satoh, Koji ; Ohtomo, Yasuhiro ; Sunako, Tomomi ; Murakami, Kazuo ; Matsubara, Kenichi ; Kawai, Jun ; Carninci, Piero ; Hayashizaki, Yoshihide ; Kikuchi, Shoshi ; Tomita, Masaru. / Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). In: Bioinformatics. 2005 ; Vol. 21, No. 9. pp. 1758-1763.

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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: We systematically identified putative alternative first exon transcripts in rice, verified the candidates using 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.",

author = "Noriyuki Kitagawa and Takanori Washio and Shunichi Kosugi and Tomoya Yamashita and Kenji Higashi and Hiroshi Yanagawa and Kenichi Higo and Koji Satoh and Yasuhiro Ohtomo and Tomomi Sunako and Kazuo Murakami and Kenichi Matsubara and Jun Kawai and Piero Carninci and Yoshihide Hayashizaki and Shoshi Kikuchi and Masaru Tomita",

note = "Funding Information: We would like to thank Hitomi Itoh, Hiromi Komai, Goki Kashima and members at the Institute for Advanced Biosciences for their help and enlightening discussions. We also thank TMRI for providing the genomic sequence data. This work was supported by the Ministry of Agriculture, Forestry and Fisheries of Japan (Rice Genome Project SY-1104). This work was also supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan, through {\textquoteleft}the 21st Century COE Program{\textquoteright} and {\textquoteleft}Special Coordination Funds Promoting Science and Technology{\textquoteright}.",

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AU - Kitagawa, Noriyuki

AU - Washio, Takanori

AU - Kosugi, Shunichi

AU - Yamashita, Tomoya

AU - Higashi, Kenji

AU - Yanagawa, Hiroshi

AU - Higo, Kenichi

AU - Satoh, Koji

AU - Ohtomo, Yasuhiro

AU - Sunako, Tomomi

AU - Murakami, Kazuo

AU - Matsubara, Kenichi

AU - Kawai, Jun

AU - Carninci, Piero

AU - Hayashizaki, Yoshihide

AU - Kikuchi, Shoshi

AU - Tomita, Masaru

N1 - Funding Information: We would like to thank Hitomi Itoh, Hiromi Komai, Goki Kashima and members at the Institute for Advanced Biosciences for their help and enlightening discussions. We also thank TMRI for providing the genomic sequence data. This work was supported by the Ministry of Agriculture, Forestry and Fisheries of Japan (Rice Genome Project SY-1104). This work was also supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan, through ‘the 21st Century COE Program’ and ‘Special Coordination Funds Promoting Science and Technology’.

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N2 - 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: We systematically identified putative alternative first exon transcripts in rice, verified the candidates using 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.

AB - 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: We systematically identified putative alternative first exon transcripts in rice, verified the candidates using 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.

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