Identification of novel siRNA pathways involved in plant environmental stress responses

2013 Fiscal Year Final Research Report

• Project/Area Number: 24657041
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Single-year Grants
• Research Field: Plant molecular biology/Plant physiology
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: SEKI Motoaki 独立行政法人理化学研究所, 環境資源科学研究センター, チームリーダー (80281624)
• Co-Investigator(Renkei-kenkyūsha): MATSUI Akihiro 独立行政法人理化学研究所, 環境資源科学研究センター, 研究員 (90443027)
• Project Period (FY): 2012-04-01 – 2013-03-31
• Keywords: 植物分子機能 / small RNA

Research Abstract

Arabidopsis transcriptome analysis under drought, cold, high-salinity stress and ABA treatment conditions, using tiling array, showed that approximately 6,000 novel transcripts existed in the antisense strand of the AGI code genes and they were induced under abiotic stress. To study the biogenesis mechanism of the antisense RNAs, accumulation of RD29A antisense RNA was analyzed, using RNA-dependent RNA polymerase (RDR) mutant series. Finally, we found that rdr1/2/6 mutation decreased accumulation of RD29A antisense RNA. RNase protection and RNA decay analyses showed that RD29A antisense RNA formed double stranded RNA and promoted degradation of RD29A mRNA. However, RNA-seq analysis did not detect siRNA accumulation in this locus. These results show that antisense RNAs are produced by RNA-dependent RNA polymerase (RDR) 1/2/6 without involving siRNA generation.

Research Products

• [Journal Article] Arabidopsis Non-coding RNA Regulation in Abiotic Stress Responses.In Special Issue"Regulation by non-coding RNAs" (2013)
  • Author(s): Matsui, A., Nguyen, A.H., Nakaminami, K. and Seki, M.
  • Journal Title: International Journal of Molecular Sciences Volume: 14 Pages: 22642-22654
  • DOI: 10.3390/ijms141122642
  • 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
  • DOI: 10.1093/bioinformatics/bts065
  • Peer Reviewed
• [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.
  • Journal Title: G3 Volume: 2 Pages: 487-498
  • DOI: 10.1534/g3.111.001362
  • Peer Reviewed
• [Presentation] Novel Epigenetic and RNA Regulation in Plant Abiotic Stress Responses (2014)
  • Author(s): Seki, M.
  • Organizer: Invited Seminar at Rockefeller Univ.
  • Place of Presentation: New York, USA (Host : Prof. Nam-Hai Chua)
  • Year and Date: 2014-01-10
• [Presentation] Novel Antisense RNA Regulation Functions in Plant Abiotic Stress Responses (2013)
  • Author(s): Matsui, A., Iida, K., Tanaka, M., Ishida, J., Morosawa, T., Takahashi, S., Toyoda, T. and Seki, M.
  • Organizer: ASPB Satellite Meeting "Post-transcriptional Gene Regulation in Plants"
  • Place of Presentation: Providence, USA
  • Year and Date: 20130725-26
• [Presentation] Novel non-coding antisense RNA regulation in plant abiotic stress responses (2013)
  • Author(s): Seki, M.
  • Organizer: International Symposium "Non-coding RNA in plants"
  • Place of Presentation: Wittenberg, Germany
  • Year and Date: 20130710-12
• [Presentation] Novel RNA and Epigenetic Regulations in Plant Abiotic Stress Responses (2013)
  • Author(s): Matsui, A., Kim, J.M., To, T.K., Iida, K., Tanaka, M., Ishida, J., Morosawa, T., Toyoda, T. and Seki, M.
  • Organizer: 2013 International Symposium on Agricultural Biotechnology : Emerging Topics on Plant Stress Biology
  • Place of Presentation: Taipei, Taiwan
  • Year and Date: 20130524-25
• [Presentation] 環境ストレス条件下での新規アンチセンスRNAの生成はRNA-dependent RNA polymeraseによって行われる (2013)
  • Author(s): 松井章浩, 飯田慶, 山口勝司, 田中真帆, 石田順子, 諸澤妙子, 重信秀治, 篠崎一雄, 豊田哲郎, 関原明
  • Organizer: 第54回日本植物生理学会年会
  • Place of Presentation: 岡山
  • Year and Date: 2013-03-21
• [Presentation] Novel antisense RNA and epigenetic regulation in plant abiotic stress responses (2013)
  • Author(s): Matsui, A., Kim, J.M., Kim To, T., Iida, K., Tanaka, M., Ishida, J., Morosawa, T., Toyoda, T. and Seki, M.
  • Organizer: Abiotic Stress Workshop, Plant & Animal Genome ASIA 2013
  • Place of Presentation: Singapore
  • Year and Date: 2013-03-18
• [Presentation] Novel non-coding antisense RNA regulation in plant abiotic stress responses (2012)
  • Author(s): Matsui, A., Iida, K., Tanaka, M., Ishida, J., Morosawa, T., Toyoda, T. and Seki, M.
  • Organizer: Cold Spring Harbor Conferences Asia, Plany Epigenetics, Stress and Evolution
  • Place of Presentation: Suzhou, China
  • Year and Date: 20121029-1102
• [Presentation] Stress-inducible non-coding antisense RNAs are generated by RDR-mediated RNA dopying mechanism and function in the turnover of the sense mRNAs under abiotic stress (2012)
  • Author(s): Matsui, A., Iida, K., Yamaguchi, K., Tanaka, M., Ishida, J., Morosawa, T., Kim, J.-M., Shigenobu, S., Shinozaki, K., Toyoda, T. and Seki, M.
  • Organizer: International Plant RNA Workshop 2012
  • Place of Presentation: Vienna, Austria
  • Year and Date: 20120708-09
• [Presentation] Novel RNA and epigenetic regulation in plant abiotic stress responses (2012)
  • Author(s): Seki, M.
  • Organizer: GNU Plant Science Symposium 2012
  • Place of Presentation: Jinju, Korea
  • Year and Date: 20120510-12
• [Presentation] Biogenesis mechanism and function of stress-inducible non-protein-coding antisense RNAs in Arabidopsis (2012)
  • Author(s): Seki, M., Iida, K., Yamaguchi, K., Tanaka, M., Ishida, J., Morosawa, T., Shigenobu, S., Shinozaki, K., Toyoda, T. and Matsui, A.
  • Organizer: BIT's 3rd Annual World on DNA and Genome day
  • Place of Presentation: Xi'an, China
  • Year and Date: 20120425-28
• [Presentation] Novel RNA and Epigenetic Regulation in Plant Abiotic Stress Responses (2012)
  • Author(s): Seki, M.
  • Organizer: Seminar at University of Cambridge
  • Place of Presentation: Cambridge, UK
  • Year and Date: 2012-12-13
• [Presentation] Novel antisense RNA and epigenetic regulations in plant abiotic stress responses (2012)
  • Author(s): Seki, M.
  • Organizer: School of Biological Sciences Seminar, Royal Holloway, University of London
  • Place of Presentation: Egham, UK
  • Year and Date: 2012-12-12
• [Presentation] Novel posttranscriptional and epigenetic regulation in plant abiotic stress responses (2012)
  • Author(s): Seki, M.
  • Organizer: Workshops on Biotechnology Research and Application in Agriculture2
  • Place of Presentation: AGI, Ha Noi, Viet Nam
  • Year and Date: 2012-09-05
• [Presentation] Novel RNA and epigenetic regulation in plant abiotic stress responses, and Establishiment of cassava functional genomics platform and its application to molecular breeding (2012)
  • Author(s): Seki, M.
  • Organizer: Seminar at Hanoi University of Agriculture
  • Place of Presentation: Hanoi University of Agriculture, Ha Noi, Vietnam
  • Year and Date: 2012-06-09
• [Remarks] 理化学研究所環境資源科学研究センター植物ゲノム発現研究チーム
  • URL: http://www.csrs.riken.jp/jp/labs/pgnrt/index.html