Analysis of stress-responsive non-coding antisense RNAs that are co-expressed with sense RNAs

• Project/Area Number: 21570056
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Plant molecular biology/Plant physiology
• Research Institution: The Institute of Physical and Chemical Research
• Principal Investigator: SEKI Motoaki 独立行政法人理化学研究所, 植物ゲノム発現研究チーム, チームリーダー (80281624)
• Co-Investigator(Renkei-kenkyūsha): TOYODA Tetsuro 独立行政法人理化学研究所, 生命情報基盤研究部門, 部門長 (20342818) ; MATSUI Akihiro 独立行政法人理化学研究所, 植物ゲノム発現研究チーム, 研究員 (90443027)
• Project Period (FY): 2009 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2011: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2010: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2009: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
• Keywords: 植物 / ゲノム / ストレス / 発現制御 / 非翻訳型RNA / アンチセンスRNA / RNA-dependent RNA polymerase / RNA制御 / 環境ストレス応答 / small RNA / シロイヌナズナ / タイリングアレイ解析 / 非翻訳性RNA

Research Abstract

Our previous study identified about 7, 000 stress-inducible antisense RNAs in Arabidopsis and showed that RD29A locus that has typical drought-inducible gene, has a type of stress-inducible antisense RNA which is complementary to sequence of the sense mRNA. Real time RT-PCR analysis showed that accumulation of RD29A antisense RNA was decreased in rdr1/2/6 triple mutants. Our data indicates a novel RNA regulation mechanism that RDR-mediated synthesis of antisense RNAs functions in the turnover of sense mRNAs under the stress conditions in plants.

Research Products

• [Journal Article] Surveillance of 3' non-coding transcripts requires FIERY1 and XRN3 in Arabidopsis (2012)
  • Author(s): Kurihara, Y., Schmitz, R. J., Nery, J. R., Schultz, M. D., Okubo-Kurihara, E., Morosawa, T., Tanaka, M., Toyoda, T., Seki, M. and Ecker, J. R.
  • Volume: G3 2
  • Pages: 487-498
  • Peer Reviewed
• [Journal Article] Positional correlation analysis improves reconstruction of full-length transcript and alternative isoform from noisy array signals or short reads (2012)
  • Author(s): Kawaguchi, S., Iida, K., Harada, E., Hanada, K., Matsui, A., Okamoto, M., Shinozaki, K., Seki, M. and Toyoda, T.
  • Journal Title: Bioinformatics Volume: 28 Pages: 929-937
  • Peer Reviewed
• [Journal Article] RNA regulation in plant abiotic stress responses (2012)
  • Author(s): Nakaminami, K., et al
  • Journal Title: BBA-Gene Regulatory Mechanisms Volume: (in press)
  • Peer Reviewed
• [Journal Article] Positional correlation analysis improves reconstruction of full-length transcript and alternative isoform from noisy array signals or short reads (2012)
  • Author(s): Kawaguchi, S., et al
  • Journal Title: Bioinformatics Volume: (in press)
  • Peer Reviewed
• [Journal Article] RNA regulation in plant abiotic stress responses (2011)
  • Author(s): Nakaminami, K., Matsui, A., Shinozaki, K. and Seki, M.
  • Journal Title: BBA-Gene Regulatory Mechanisms Volume: 19 Pages: 149-153
  • Peer Reviewed
• [Journal Article] Expression profile and 5'-terminal structure of Arabidopsis antisense transcripts expressed in seeds (2011)
  • Author(s): Okamoto, M. and Seki, M
  • Journal Title: Plant Signaling Behavior Volume: 6 Pages: 691-693
  • Peer Reviewed
• [Journal Article] ARTADE2DB : Improved Statistical Inferences for Arabidopsis Gene Functions and Structure Predictions by Dynamic-Structure-Based Dynamic Expression(DSDE) Analyses (2011)
  • Author(s): Iida, K., Kawaguchi, S., Kobayashi, N., Yoshida, Y., Ishii, M., Harada, E., Hanada, K., Matsui, A., Okamoto, M., Seki, M. and Toyoda, T.
  • Journal Title: Plant Cell Physiol Volume: 52 Pages: 254-264
  • NAID: 10029708540
  • Peer Reviewed
• [Journal Article] Expression profile and 5'-terminal structure of Arabidopsis antisense transcripts that are expressed in seeds. (2011)
  • Author(s): Okamoto, et al.
  • Journal Title: Plant Signaling Behavior Volume: (in press)
  • Peer Reviewed
• [Journal Article] ARTADE2DB : Improved Statistical Inferences for Arabidopsis Gene Functions and Structure Predictions by Dynamic-Structure-Based Dynamic Expression (DSDE) Analyses. (2011)
  • Author(s): Iida, et al.
  • Journal Title: Plant and Cell Physiology Volume: (in press)
  • Peer Reviewed
• [Journal Article] Omics' analyses of regulatory networks in plant abiotic stress responses (2010)
  • Author(s): Urano, K., Kurihara, Y., Seki, M. and Shinozaki, K.
  • Journal Title: Current Opin Volume: 13 Pages: 132-138
  • Peer Reviewed
• [Journal Article] Arabidopsis tiling array analysis to identify the stress-responsive genes. (2010)
  • Author(s): Matsui, et al.
  • Journal Title: Methods in Molecular Biology-Plant Stress Tolerance (Edited by R.Sunkar) Volume: 639 Pages: 141-155
• [Journal Article] 'Omics' analyses of regulatory networks in plant abiotic stress responses (2010)
  • Author(s): Urano, K.
  • Journal Title: Current Opin.Plant Biol. (in press)
  • Peer Reviewed
• [Journal Article] Functional genomics using RIKEN Arabidopsis thaliana Full-Length(RAFL)cDNAs (2009)
  • Author(s): Seki, M.
  • Journal Title: J.Plant Res. 122 Pages: 355-366
  • Peer Reviewed
• [Presentation] Biogenesis mechanism and function of stress-inducible non-coding antisense RNAs (2012)
  • Author(s): Seki, M., et al
  • Organizer: 第53回日本植物生理学会年会シンポジウム
  • Place of Presentation: 京都産業大学(京都市)(招待講演)
  • Year and Date: 2012-03-17
• [Presentation] RNA-dependent RNA polymeraseにより、環境ストレス下でアンチセンスRNAが生成する (2012)
  • Author(s): 松井章浩, ら
  • Organizer: 第53回日本植物生理学会年会
  • Place of Presentation: 京都産業大学(京都市)
  • Year and Date: 2012-03-17
• [Presentation] RNA masking system during cold deacclimation of Arabidopsis plants (2011)
  • Author(s): Nakaminami, K., Minami, A., Nakagami, H., Nomura, Y., Tanaka, M., Morosawa, T., Ishida, J., Shirasu, K., Uemura, M. and Seki, M.
  • Organizer: International Plant RNA Workshop 2011
  • Place of Presentation: Yokohama
  • Year and Date: 2011-06-21
• [Presentation] Biogenesis mechanism and function of stress-inducible non-coding antisense RNAs (2011)
  • Author(s): Matsui, A., Ishida, J., Morosawa, T., Tanaka, M., Endo, T. A., Iida, K., Toyoda, T., Shinozaki, K. and Seki, M.
  • Organizer: International Plant RNA Workshop 2011
  • Place of Presentation: Yokohama
  • Year and Date: 2011-06-20
• [Presentation] A survey and analysis of regulated alternative splicing events in Arabidopsis thaliana using genome tiling array and mRNA-seq (2011)
  • Author(s): Iida, K., Kawaguchi, S., Harada, E., Matsui, A., Seki, M. and Toyoda, T.
  • Organizer: International Plant RNA Workshop 2011
  • Place of Presentation: Yokohama
  • Year and Date: 2011-06-20
• [Presentation] Biogenesis mechanism and function of stress-inducible non-coding antisense RNAs (2011)
  • Author(s): Matsui, A., et al
  • Organizer: International Plant RNA Workshop 2011
  • Place of Presentation: 理研横浜研究所(横浜市)(招待講演)
  • Year and Date: 2011-06-20
• [Presentation] A survey and analysis of regulated alternative splicing events in Arabidopsis thaliana using genome tiling array and mRNA-seq (2011)
  • Author(s): Iida, K., et al
  • Organizer: International Plant RNA Workshop 2011
  • Place of Presentation: 理研横浜研究所(横浜市)(招待講演)
  • Year and Date: 2011-06-20
• [Presentation] センス鎖遺伝子と共発現するストレス応答性のアンチセンスRNAの生成機構の解析 (2011)
  • Author(s): 松井章浩, ら
  • Organizer: 第52回日本植物生理学会年会
  • Place of Presentation: 東北大学(仙台)
  • Year and Date: 2011-03-20
• [Presentation] Novel RNA and chromatin regulation in plant abiotic stress responses (2011)
  • Author(s): Seki, et al.
  • Organizer: Plant & Animal Genome XIX.
  • Place of Presentation: Town and Country Resort(サンディエゴ、米国)
  • Year and Date: 2011-01-16
• [Presentation] Novel RNA and chromatin regulation in plant abiotic stress responses (2011)
  • Author(s): Matsui, A., Kim, J. M., To, K. T., Nakaminami, K., Ishida, J., Morosawa, T., Tanaka, M., Kobayashi, S., Nishioka, T., Ushifusa, C., Shinozaki, K., Toyoda, T. and Seki, M.
  • Organizer: Abiotic Stress Workshop, Plant & Animal Genome XIX. The International Conference on the Status of Plant & Animal Genome Research
  • Place of Presentation: San Diego, USA
• [Presentation] Novel RNA- and chromatin remodeling-mediated regulatory mechanisms in plant abiotic stress responses (2010)
  • Author(s): Seki, et al.
  • Organizer: The 2010 Cold Spring Harbor Asia Conference on From Plant Biology to Crop Biotechnology
  • Place of Presentation: Suzhou Dushu Lake Conference Center(蘇州、中国)
  • Year and Date: 2010-10-28
• [Presentation] Genome-wide analysis of RNA regulation in plant abiotic stress responses (2010)
  • Author(s): Seki, et al.
  • Organizer: Society for Experimental Biology, Annual Main Meeting 2010
  • Place of Presentation: The Clarion Congress Hotel(ブラハ、チエコ)
  • Year and Date: 2010-07-03
• [Presentation] Transcriptome analysis in abiotic stress conditions using Arabidopsis whole genome tiling array (2010)
  • Author(s): Matsui, et al.
  • Organizer: 21^<st> International Conference on Arabidopsis Research
  • Place of Presentation: パシフィコ横浜(横浜市)
  • Year and Date: 2010-06-06
• [Presentation] Tiling array analysis under drought, cold, high-salinity and ABA treatment revealed the existence of sense-antisense transcripts of possible regulatory roles in Arabidopsis (2010)
  • Author(s): Matsui, A.
  • Organizer: Keystone Symposia, RNA Silencing Mechanisms in Plants
  • Place of Presentation: サンタフェ(米国)
  • Year and Date: 2010-02-22
• [Presentation] Novel RNA-and chromatin remodeling-mediated regulatory mechanisms in plant abiotic stress responses (2010)
  • Author(s): Matsui A., Kim J-M., To K. T., Nakaminami K., Ishida J., Morosawa T., Tanaka M., Endo T., Kawaguchi S., Iida K., Shinozaki K., Toyoda T. and Seki, M.
  • Organizer: The 2010 Cold Spring Harbor Asia Conference on From Plant Biology to Crop Biotechnology
  • Place of Presentation: Suzhou, China
• [Presentation] Genome-wide analysis of RNA regulation in plant abiotic stress responses (2010)
  • Author(s): Seki, M., Matsui A., Ishida J., Morosawa T., Iida K., Endo T., Okamoto M., Tanaka M., Kawaguchi S., Shinozaki K. and Toyoda T.
  • Organizer: Society for Experimental Biology Annual Main Meeting 2010
  • Place of Presentation: Prague Czech Republic
• [Presentation] A computational elucidation of the transcriptional dynamics in Arabidopsis thaliana from comprehensive use of tiling array experiments (2009)
  • Author(s): 川口修治
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 横浜市
  • Year and Date: 2009-12-09
• [Presentation] Novel RNA- and chromatin remodeling- mediated regulatory mechanisms in plant abiotic stress responses (2009)
  • Author(s): Matsui, A.
  • Organizer: 9th IPMB Congress
  • Place of Presentation: セントルイス(米国)
  • Year and Date: 2009-10-26
• [Presentation] Novel RNA- and chromatin remodeling- mediated regulatory mechanisms in plant abiotic stress responses (2009)
  • Author(s): Matsui, A.
  • Organizer: 20th International Conference on Arabidopsis Research
  • Place of Presentation: エジンバラ(英国)
  • Year and Date: 2009-07-03
• [Presentation] ARTADE2.0 : a mathematical integration of tiling array, CAGE and sequeince data to elucidate the transcriptional systems dynamics of Arabidonsis thaliana (2009)
  • Author(s): 川口修治
  • Organizer: 20th International Conference on Arabidonsis Research
  • Place of Presentation: エジンバラ(英国)
  • Year and Date: 2009-07-01
• [Presentation] Novel RNA-and chromatin remodeling-mediated regulatory mechanisms in plant abiotic stress resonses (2009)
  • Author(s): Matsui A., Kim J-M., Ishida J., Morosawa T., Endo T., Okamoto M., Kurihara K., Nakaminami K., Tanaka M., To T., Nambara E., Hanada K., Mochizuki Y., Kawaguchi S., Toyoda T., Shinozak K. and Seki M.
  • Organizer: 9th IPMB Congress
  • Place of Presentation: St. Louis, Missouri, USA
• [Presentation] Novel RNA-and chromatin remodelingmediated regulatory mechanisms in plant abiotic stress resonses (2009)
  • Author(s): Matsui A., Kim J-M., Ishida J., Morosawa T., Okamoto M., Kim T., Nambara E., Mochizuki Y., Kawaguchi S., Toyoda T., Shinozak K. and Seki M.
  • Organizer: 20th International Conference on Arabidopsis Research
  • Place of Presentation: Edinburgh, Scotlant UK
• [Presentation] ARTADE2.0 : a mathematical integration of tiling array, CAGE and sequeince data to elucidate the transcriptional systems dynamics of Arabidopsis thaliana (2009)
  • Author(s): Kawaguchi S., Hanada K., Iida K., Mochizuki Y., Matsui A., Okamoto M., Seki M., Shinozaki K. and Toyoda T.
  • Organizer: 20th International Conference on Arabidopsis Research
  • Place of Presentation: Edinburgh, Scotlant UK
• [Presentation] Multiple alternative splicing events in individual transcripts ; analyses using full-length cDNAs and tiling arrays (2009)
  • Author(s): Iida K., Kawaguchi S., Nanada K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M., Shinozaki K. and Toyoda T.
  • Organizer: 20th International Conference on Arabidopsis Research
  • Place of Presentation: Edinburgh, Scotlant UK
• [Book] Genome-wide analysis of RNA degradation in Arabidopsis. In "RNA Technologies(Edited by Volker A. Erdmann and Jan Barciszewski)" (2011)
  • Author(s): Kurihara, Y. and Seki, M.
  • Publisher: Springer Publisher
• [Book] RNA Technologies(Edited by Volker A.Erdmann and Jan Barciszewski) (2011)
  • Author(s): Kurihara, Y., Seki, M.
  • Publisher: Springer Publisher
• [Book] Arabidopsis tiling array analysis to identify the stress-responsive genes. In "Methods in Molecular Biology-Plant Stress Tolerance(Edited by Dr. Ramanjulu Sunkar)" (2010)
  • Author(s): Matsui, A., Ishida, J., Morosawa, T., Okamoto, M., Kim, J. M., Kurihara, Y., Kawashima, M., Tanaka, M., To, T., Nakaminami, K., Kaminuma, E., Endo, T., Mochizuki, Y., Kawaguchi, S., Kobayashi, N., Toyoda, T., Shinozaki, K. and Seki, M.
  • Publisher: Humana Press
• [Book] Methods in Molecular Biology-Plant Stress Tolerance (2010)
  • Author(s): Matsui, A.
  • Publisher: Humana Press Inc.(in press)
• [Remarks]
  • URL: http://labs.psc.riken.jp/pgnrt/
• [Remarks]
  • URL: http://labs.psc.riken.jp/pgnrt/
• [Remarks]
  • URL: http://labs.psc.riken.jp/pgnrt/