Analysis of mRNA fates with exclusive function mediated by RNA granules

• Project/Area Number: 15H04628
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Applied molecular and cellular biology
• Research Institution: The University of Tokyo
• Principal Investigator: Watanabe Yuichiro 東京大学, 大学院総合文化研究科, 教授 (60183125)
• Co-Investigator(Kenkyū-buntansha): 濱田 隆宏 東京大学, 大学院総合文化研究科, 助教 (20452534)
• Co-Investigator(Renkei-kenkyūsha): Sato Masanao 北海道大学, 大学院農学研究科, 助教 (20517693) ; Okamoto Akimitsu 東京大学, 先端科学技術研究センター, 教授 (60314233)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥15,600,000 (Direct Cost: ¥12,000,000、Indirect Cost: ¥3,600,000); Fiscal Year 2017: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000); Fiscal Year 2016: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2015: ¥7,280,000 (Direct Cost: ¥5,600,000、Indirect Cost: ¥1,680,000)
• Keywords: 植物 / mRNA制御 / 環境応答 / 高温ストレス / ストレス顆粒 / P-ボディー / RNA顆粒 / シロイヌナズナ / mRNa分解 / 翻訳抑制 / イネ / 野外環境 / 生体機能利用 / 環境対応 / 気候変動 / 環境調和型農林水産 / mRNA分解 / 脱キャップ酵素 / ストレス / バイオテクノロジー / プロセッシングボディー / RNAプロファイリング

Outline of Final Research Achievements

We have studied dynamic changes of P-bodies and stress granules (SG) in Arabidopsis before and after heat stress application. DCP2 (decapping enzyme 2; P-body marker) began to accumulate to cytoplasmic granules preformed by DCP1, while eIF4A2 (SG marker) started to form granules independently from DCP1/2. SG often came close to P-bodies over time, and some time later it detached the contact with P-bodies. We also analyzed the RNA species of which levels were elevated and those lessened after temperature rises. It turned out that almost 7000 RNA species increased and almost the same number of RNA species decreased by heat stress. It meant that 30% of total genes were transcriptionally activated while another 30% of mRNAs were specifically destabilized. When the temperature returned normal, about half member of each gene set showed reciprocal pattern in accumulation. The phosphorylation level of DCP1 reflects the rise of temperature and is likely to be involved in DCP2 accumulation.

Research Products

• [Int'l Joint Research] Monash University(オーストラリア)
• [Int'l Joint Research] University of California, Davis(アメリカ)
• [Int'l Joint Research] Max Planck Institute(ドイツ)
• [Int'l Joint Research] モナシュ大学(オーストラリア)
• [Journal Article] The GYF domain protein PSIG1 dampens the induction of cell death during plant-pathogen interactions. (2017)
  • Author(s): Matsui, H., Nomura, Y., Egusa, M., Hamada, T., Hyon, G-S., Kaminaka, H., Watanabe, Y., Ueda, T., Trujillo, M., Shirasu, K., Nakagami, H.
  • Journal Title: PLoS Genetics Volume: -
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Insights into land plant evolution garnered from the Marchantia polymorpha genome (2017)
  • Author(s): Bowman J, Kouchi T,..(106名）..Yokoyama R, ..(4名)
  • Journal Title: Cell Volume: 171 Pages: 287-304
  • DOI: 10.1016/j.cell.2017.09.030
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 植物におけるRNA顆粒 (2017)
  • Author(s): 濱田隆宏，渡邊雄一郎
  • Journal Title: 植物科学最前線 Volume: 8 Pages: 99-109
  • Peer Reviewed / Open Access
• [Journal Article] 陸上植物を小分子RNAとRNAサイレンシング機能からみたとき (2017)
  • Author(s): 渡邊雄一郎
  • Journal Title: 生物科学 Volume: 68 Pages: 196-205
  • Peer Reviewed
• [Journal Article] Light perception in aerial tissues activates DWF4 expression in root tips and induces root growth (2017)
  • Author(s): Sakaguchi, J and Watanabe, Y
  • Journal Title: Scientific Reports Volume: 7 Pages: 1808-1808
  • DOI: 10.1038/s41598-017-01872-4
  • Peer Reviewed / Open Access
• [Journal Article] The naming of names: Guidelines for gene nomenclature in Marchantia (2016)
  • Author(s): Bowman, J., Araki, T., Arteaga-Vazquez, M., Berger, F., Dolan, L., Haseloff, J., Ishizaki, K., Kyozuka, J., Lin, S.S., Nagasaki, H., Nakagami, H., Nakajima, K., Nakamura, Y., Ohashi-Ito, K., Sawa, S., Shimamura, M., Solano, R., Tsukaya, H., Ueda, T., Watanabe, Y., Yamato, K.T., Zachgo, S., and Kohchi, T.
  • Journal Title: Plant Cell Physiol Volume: 57 Pages: 257-261
  • DOI: 10.1093/pcp/pcv193
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Profiling and characterization of small RNAs in the liverwort, Marchantia polymorpha, belonging to the first diverged land plants. (2016)
  • Author(s): Masayuki Tsuzuki, Ryuichi Nishihama, Kimitsune Ishizaki, Yukio Kurihara, Minami Matsui, John L. Bowman, Takayuki Kohchi, Takahiro Hamada, and Yuichiro Watanabe
  • Journal Title: Plant & Cell Physiology Volume: 57(2) Pages: 359-372
  • DOI: 10.1093/pcp/pcv182
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] <i>Arabidopsis</i> AtRRP44 has ribonuclease activity that is required to complement the growth defect of yeast <i>rrp44</i> Mutant (2016)
  • Author(s): Kumakura, N., Otsuki, H., Ito, M. et al.
  • Journal Title: Plant Biotechnology Volume: 33 Issue: 2 Pages: 77-85
  • DOI: 10.5511/plantbiotechnology.16.0316a
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] 植物成長段階の切替えスイッチとしてのmiRNA (2016)
  • Author(s): 都筑正行、濱田隆宏、渡辺雄一郎
  • Journal Title: 現代化学 Volume: N/A Pages: 46-50
• [Journal Article] Diffuse DCP2 Accumulates in DCP1 Granules under Heat Stress in Arabidopsis thaliana. (2015)
  • Author(s): Motomura K, Le TN. Q, Hamada T, Kutsuna N, Mano S, Nishimura M and Watanabe Y.
  • Journal Title: Plant Cell Physiol Volume: 56 Pages: 107-115
  • DOI: 10.1093/pcp/pcu151
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] Liverwort life cycle and the miRNAs (2018)
  • Author(s): Masayuki Tsuzuki, Kazutaka Futagami, Takahiro Hamada, Yuichiro Watanabe
  • Organizer: 第59回日本植物生理学会年会
  • Int'l Joint Research / Invited
• [Presentation] Functional Analysis of miR319 in liverwort, Marchantia polymorpha (2017)
  • Author(s): 二神和敬, 都筑正行、濱田隆宏、渡邊雄一郎
  • Organizer: 第19回日本RNA学会年会
• [Presentation] Lessons from biotic and abiotic stress studies (2017)
  • Author(s): Yuichiro Watanabe
  • Organizer: Future prospects of control measures for plant disease and insect pests for sustainable crop production
  • Int'l Joint Research / Invited
• [Presentation] 温度変化に応答した微小管ダイナミクス (2017)
  • Author(s): 濱田隆宏、渡邊雄一郎
  • Organizer: 日本植物学会第81回大会
• [Presentation] 第一回RNA顆粒・RNAタンパク質複合体研究会 (2016)
  • Author(s): 濱田隆宏
  • Organizer: 第一回RNA顆粒・RNAタンパク質複合体研究会
  • Place of Presentation: 基礎生物学研究所（愛知県岡崎市）
  • Invited
• [Presentation] ゼニゴケの小分子RNA解析からみえる陸上植物の発生制御モジュール (2016)
  • Author(s): 渡邊 雄一郎、都筑 正行、濱田 隆宏、河内 孝之、John L. Bowman
  • Organizer: 第39回日本分子生物学会年会
  • Place of Presentation: 横浜パシフィコ（神奈川県横浜市）
  • Year and Date: 2016-11-30
  • Invited
• [Presentation] 顕微鏡を基盤とした初期発生におけるmRNA分解機構の比較解析 (2016)
  • Author(s): 元村一基、丸山大輔、栗原大輔、熊倉直祐、渡邊雄一郎、東山哲也
  • Organizer: 日本植物学会第80回大会
  • Place of Presentation: 沖縄コンベンションセンター（沖縄県宜野湾市）
  • Year and Date: 2016-09-16
• [Presentation] 陸上植物に保存されたmicroRNAによる発生制御機構 (2016)
  • Author(s): 都筑正行、濱田隆宏、渡邊雄一郎
  • Organizer: 日本植物学会第80回大会
  • Place of Presentation: 沖縄コンベンションセンター（沖縄県宜野湾市）
  • Year and Date: 2016-09-16
  • Invited
• [Presentation] Imaging Analysis in roles of mRNA decay at early plant development (2016)
  • Author(s): Motomura, K., Maruyama, D., Kurihara, D., Watanabe, Y., Higashiyama, T.
  • Organizer: 第21回RNA Society国際会議
  • Place of Presentation: 京都国際会議場 （京都府京都市）
  • Year and Date: 2016-06-28
  • Int'l Joint Research
• [Presentation] Communication between nucleus and cytoplasm through RNA-interacting proteins (2016)
  • Author(s): Yuichiro Watanabe, Takahiro Hamada
  • Organizer: The 57th Annual Meeting of the Japanese Society of Plant Physiologists
  • Place of Presentation: 岩手大学（岩手県盛岡市）
  • Year and Date: 2016-03-18
  • Int'l Joint Research / Invited
• [Presentation] Analysis of TARP mediated-siRNA biosynthesis in Arabidopsis (2016)
  • Author(s): Tsukada, M., Tsuzuki, M., Fukao, Y., Kurihara, Y., Matsui, M., Motomura, K., Tamura, K., Hara-Nishimura, I., Watanabe, Y., Hamada, T.
  • Organizer: 日本植物生理学会
  • Place of Presentation: 岩手大学（岩手県盛岡市）
  • Year and Date: 2016-03-18
  • Int'l Joint Research
• [Presentation] Characterization of small RNAs in a liverwort, Marchantia polymorpha (2015)
  • Author(s): Masayuki Tsuzuki, Tsuyoshi Fujimoto, Ryuichi Nishihama, Kimitsune Ishizaki, Yukio Kurihara, Minami Matsui, Takayuki Kohchi, Takahiro Hamada, Yuichiro Watanabe
  • Organizer: EMBO Symposium "The Non-Coding Genome"
  • Place of Presentation: EMBL ( Heidelberg, ドイツ）
  • Year and Date: 2015-10-18
  • Int'l Joint Research
• [Presentation] 苔類ゼニゴケにおけるmicroRNAの機能解析 (2015)
  • Author(s): 都筑正行，藤本剛史、西浜竜一、石崎公庸、栗原志夫、松井南、河内孝之、濱田隆宏、渡邊雄一郎
  • Organizer: 日本植物学会第79回大会
  • Place of Presentation: 朱鷺メッセ（新潟県新潟市）
  • Year and Date: 2015-09-06
• [Book] Plant Epigenetics: Methods and Protocols (2016)
  • Author(s): Tsuzuki, M. and Watanabe, Y.
  • Total Pages: 22
  • Publisher: Springer
• [Remarks] ストレスに応答して現れるRNA顆粒の解析
  • URL: http://park.itc.u-tokyo.ac.jp/RNAwatanabe/study.html
• [Remarks] 陸上植物の多様性と遺伝子発現制御 ― evolution and gene regulation
  • URL: http://park.itc.u-tokyo.ac.jp/RNAwatanabe/study.html
• [Remarks] 環境変化によるストレス応答に対してのRNA顆粒による遺伝子発現制御
  • URL: http://park.itc.u-tokyo.ac.jp/RNAwatanabe/study.html
• [Remarks] ゼニゴケの発生過程における小分子RNAを介した遺伝子発現制御
  • URL: http://park.itc.u-tokyo.ac.jp/RNAwatanabe/study.html
• [Funded Workshop] The 57th Annual Meeting of the Japanese Society of Plant Physiologists (2016)
  • Place of Presentation: Iwate University, Morioka, Iwata, Japan
  • Year and Date: 2016-03-18