2007 Fiscal Year Final Research Report Summary
Diversity and functional differentiation of preinitiation complex of transcription in plants
| Project/Area Number |
17370017
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
植物生理・分子
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| Research Institution | Nagoya University |
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Principal Investigator |
OBOKATA Junichi Nagoya University, Center for Gene Research, Associate Professor (50185667)
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| Project Period (FY) |
2005 – 2007
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| Keywords | plant genome / preinitiation complex / core promoter / transcriptional regulation / trancription start site |
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| Research Abstract |
Core promoter is a region where preinitiation complex containing RNA polymerase II assembles, and located around the transcription start sites. However, the majority of plant promoters do not have any recognizable core promoter elements, which reflects our limited understanding of plant promoters.
We hut:la fed this grant project by elucidating the core promoter architecture of the plant genome. For this sake, we took the combined approach of in silico detection of novel core promoter elements and large-scale determination of transcription start sites (TSSs). We developed a novel methodology for TSS identification, using a combination of the Cap-Trapper and Massively Parallel Signature Sequencing methods. This technique, CT-MPSS, allowed us to identify 158,237 Arabidopsis TSS tags corresponding to 38,311 TSS loci, which has provided an opportunity for quantitative analysis of plant promoters for the first time. The expression characteristics of these core promoters were analyzed in resp
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ect to core promoter elements detected. by our in silico analyses, revealing that Arabidopsis promoters contain two major types with exclusive characteristics, a TATA type and a GA type. The TATA-type promoters tend to be associated with the Y Patch and Inr, and cause high-level expression with TSS clusters of sharp peak. By contrast, the GA type produces broad-type TSS clusters. Unlike mammalian promoters, plant promoters are not associated with CpG islands. However, plant-specific GA-type promoters share some characteristics with mammalian CpG-type promoters
Next, we examined the functional differentiation of core promoter elements with respect to tissue-specific and light-responsive transcriptional regulation, using Arabidopsis photosynthesis genes as a model case. We made a series of swapping constructs of regulatory and core promoter segments from various genes, and their reporter fusions were introduced into plants. Analysis of the expression characteristics of these chimeric promoter constructs revealed that upstream regulatory elements each have preference to specific type of core promoter subtypes. This finding implies that the functional differentiation of core promoter subtypes may reflect the functional differentiation of transcriptional preinitiation complexes. Less
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[Journal Article] Three novel subunits of Arabidopsis chloroplastic NAD (P) H dehydroge nase identified by bioinformatic and reverse genetic approaches.2009
Author(s)
Takabayashi, A., Ishikawa, N., Obayashi, T., Ishida, S., Obokata, J, Endo, T., Sato, F.
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Journal Title
Plant J 57
Pages: 207-219
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Heterogeneity of Arabidopsis core promoters revealed by high density TSS analysis.2009
Author(s)
Yamamoto, YY., Yoshitsugu, T., Sakurai, T., Seki, M., Shinozaki, K., Obokiata, J.
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Journal Title
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Three novel subunits of Arabidopsis chloroplastic NAD(P)H dehydrogenase identified by bioinformatic and reverse genetic approaches.2009
Author(s)
Takabayashi, A., Ishikawa, N., Obayashi, T., Ishida, S., Obokata. J., Endo, T., Sato, F.
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Journal Title
Plant J. 57
Pages: 207-219
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Heterogeneity of Arabidopsis core promoters revealed by high density TSS analysis.2009
Author(s)
Yamamoto, YY., Yoshitsugu, T., Sakurai, T., Seki, M., Shinozaki, K. Obokata, J.
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Journal Title
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Two RNA editing sites with cis-acting elements of moderate sequence identity are recognized by an identical site-recognition protein in tobacco chloroplasts.2008
Author(s)
Kobayashi, Y., Matsuo, M., Sakamoto, K., Wakasugi, T., Yamdada, K., Obokata, J.
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Journal Title
Nucleic Acids Res 36
Pages: 311-318
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] A site recognition factor recognizes two RNA editing sites in tobacco chloroplasts: Its implication for the diversification of plant organellar RNA editing sites.2008
Author(s)
Kobayashi, Y., Matsuo, M., Sakamoto, K., Wakasugi, T., Yamada, K., Obokata, J.
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Journal Title
Nucl. Acids Res. 36
Pages: 311-318
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Identification of plant promoter constituents by analysis of local dstribution of short sequences.2007
Author(s)
Yamamoto, YY., Ichida, H., Matsui, M., Obokata, J., Sakurai, T., Satou, M., Seki, M., Shinozaki, K., Abe, T.
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Journal Title
BMC Genomics 8
Pages: 67-89
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Identification of Plant Promoter Constituents by Analysis of Local Distribution of Short Sequences.2007
Author(s)
Yamamoto, YY., Ichida, H., Matsui, M., Obokata, J., Sakurai, T., Satou, M., Seki, M., Shinozaki, K., Abe, T.
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Journal Title
BMC Genomics 8
Pages: 67-89
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis.2007
Author(s)
Yamamoto, YY., Ichida, H., Abe, T., Suzuki, Y., Sugano, S. Obokata, J.
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Journal Title
Nucl. Acids Res. 35
Pages: 6219-6226
Description
「研究成果報告書概要(欧文)」より
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[Presentation] コード領域の上流近傍における転写開始位置の決定機構2008
Author(s)
工藤久幸, 山本義治, 中邨真之, 大谷将人, 長谷川桂子, 小保方潤一
Organizer
BMB2008(第31回日本分子生物学会年会/第81回日本生化学会大会合同大会)
Place of Presentation
神戸ポートアイランド神戸
Year and Date
20081209-20081212
Description
「研究成果報告書概要(和文)」より
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[Presentation] Promoter prediction from genome sequence2008
Author(s)
Yamamoto YY, Oboakta J
Organizer
The 55th NIBB Conference & Arabidopsis Workshop 2008 "Frontier of Plant Science in the 21st Century"
Place of Presentation
Okazaki Conference Center, Okazaki
Year and Date
20080913-20080915
Description
「研究成果報告書概要(和文)」より
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[Presentation] in silico解析による動植物ゲノムのコアプロモーター構造の比較2007
Author(s)
山本義治, 市田裕之, 阿部知子, 松井南, 鈴木穣, 菅野純夫, 櫻井哲也, 佐藤将一, 関原明, 篠崎一雄, 小保方潤一
Organizer
第48回日本植物生理学会年会
Place of Presentation
松山
Year and Date
2007-03-30
Description
「研究成果報告書概要(和文)」より
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[Presentation] LDSS : Local Distribution of Short Sequences : a novel in silico approach for extraction of promoter constituents from plant and mammalian genomes.2006
Author(s)
Yoshiharu Y. Yamamoto, Hiroyuki Ichida, Minami Matsui, Junichi Obokata, Yutaka Suzuki, Sumio Sugano, Tetsuya Sakurai, Masakazu Satou, Motoaki Seki, Kazuo Shinozaki, Tomoko Abe
Organizer
The 20th Internatinal Congress of Biochemistry and Molecular Biology
Place of Presentation
Kyoto
Year and Date
20060618-20060623
Description
「研究成果報告書概要(和文)」より
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[Presentation] LDSS法によるプロモーター構成配列の抽出と動植物のプロモーター構造の比較2006
Author(s)
山本義治, 市田裕之, 阿部知子, 鈴木穣, 菅野純夫, 櫻井哲也, 佐藤将一, 関原明, 篠崎一雄, 松井南, 小保方潤一
Organizer
日本分子生物学会2006フォーラム
Place of Presentation
名古屋
Year and Date
2006-12-06
Description
「研究成果報告書概要(和文)」より
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[Presentation] 動植物ゲノムからのプロモーター構成因子の新規抽出法2006
Author(s)
山本義治, 市田裕之, 阿部知子, 鈴木穣, 菅野純夫, 櫻井哲也, 佐藤将一, 関原明, 篠崎一雄, 松井南, 小保方潤一
Organizer
日本遺伝学会第78回大会
Place of Presentation
筑波
Year and Date
2006-09-25
Description
「研究成果報告書概要(和文)」より
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