Study for coordinated growth by epidermal cell layer in Arabidopsis

• Project/Area Number: 24570051
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Plant molecular biology/Plant physiology
• Research Institution: Nara Institute of Science and Technology
• Principal Investigator: KURATA Tetsuya 奈良先端科学技術大学院大学, バイオサイエンス研究科, 准教授 (50360540)
• Co-Investigator(Renkei-kenkyūsha): SAKAMOTO Tomoaki 奈良先端科学技術大学院大学, バイオサイエンス研究科, 博士研究員 (10600132)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000); Fiscal Year 2014: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2013: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000); Fiscal Year 2012: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: シロイヌナズナ / 器官成長 / 表皮細胞 / RNA-sequencing / 協調化 / 植物 / 胚軸 / 茎 / 次世代シーケンサー / トランスクリプトーム / マイクロアレイ

Outline of Final Research Achievements

Organ growth of multicellular plant is coordinated among cells/tissues. Old and recent physiological studies showed the outer-most cell layer, epidermis, have restrictive and promotive effects on organ growth in plants.
In this study, we defined the genes whose expression were up-regulated in the epidermis layers and under the dark condition in Arabidopsis stem and/or hypocotyl tissue. For epidermis-enriched genes, specific cell layers were dissected from paraffin-embedded slices by laser. After linear amplification of small amount RNA from dissected samples, RNA-sequencing was conducted. Informatic analysis revealed that gene expression profiling was appropriate. Combined analysis with our RNA-sequencing and public microarray data defined 73 genes were up-regulated in the epidermis of stem and under the dark condition which enhances cell growth in hypocotyl (juvenile stem-like structure).

Research Products

• [Journal Article] FT-like proteins induce transposon silencing in the shoot apex during floral induction in rice (2015)
  • Author(s): Shojiro Tamaki, Hiroyuki Tsuji, Ayana Matsumoto, Akiko Fujita, Zenpei Shimatani, Rie Terada, Tomoaki, Sakamoto, Tetsuya Kurata and Ko Shimamoto
  • Journal Title: Proceedings of the National Academy of Sciences Volume: 112 Issue: 8
  • DOI: 10.1073/pnas.1417623112
  • Peer Reviewed / Open Access
• [Journal Article] A plant U-box protein, PUB4, regulates asymmetric cell division and cell proliferation in the root meristem. (2015)
  • Author(s): Kinoshita, A, Hove, C.A., Tabata, R., Yamada, M., Shimizu, N., Ishida, T., Yamaguchi K., Shigenobu, S., Takebayashi, Y., Iuchi, S., Kobayashi, M., Kurata, T., Wada, T., Seo, M., Hasebe, M., Bilou, I., Fukuda, H., Scheres, B., Heidstra, R., Sawa, S.
  • Journal Title: Development Volume: 142 Issue: 3 Pages: 444-453
  • DOI: 10.1242/dev.113167
  • Peer Reviewed / Open Access
• [Journal Article] WOX13-like genes are required for reprogramming of leaf and protoplast cells into stem cells in the moss Physcomitrella patens. (2014)
  • Author(s): Keiko Sakakibara, Pascal Reisewitz, Tsuyoshi Aoyama, Thomas Friedrich, Sayuri Ando, Yoshikatsu Sato, Yosuke Tamada, Tomoaki Nishiyama, Yuji Hiwatashi, Tetsuya Kurata, Masaki Ishikawa, Hironori Deguchi, Stefan A. Rensing, Wolfgang Werr, Takashi Murata, Mitsuyasu Hasebe, Thomas Laux
  • Journal Title: Development Volume: 141 Issue: 8 Pages: 1660-1670
  • DOI: 10.1242/dev.097444
  • Peer Reviewed / Open Access
• [Journal Article] Contribution of NAC transcription factors to plant adaptation to land. (2014)
  • Author(s): Xu, B., Ohtani, M., Yamaguchi, M., Toyooka, K., Wakazaki, M., Sato, M., Kubo, M., Nakano, Y., Sano, R., Hiwatashi, Y., Murata, T., Kurata, T., Yoneda, A., Kato, K., Hasebe, M., and Demura, T.
  • Journal Title: Science Volume: 343 Issue: 6178 Pages: 1505-1508
  • DOI: 10.1126/science.1248417
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] System for stable b-estradiol-inducible gene expression in the moss Physcomitrella patens (2013)
  • Author(s): Minoru Kubo, Akihiro Imai, Tomoaki Nishiyama, Masaki Ishikawa, Yoshikatsu Sato, Tetsuya Kurata, Yuji Hiwatashi, Ralf Reski and Mitsuyasu Hasebe
  • Journal Title: PLoS ONE Volume: 8 Issue: 9 Pages: e77356-e77356
  • DOI: 10.1371/journal.pone.0077356
  • Peer Reviewed
• [Journal Article] High resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq (2013)
  • Author(s): Onuma Chumsakul, Kensuke Nakamura, Tetsuya Kurata, Tomoaki Sakamoto, Jon L. Hobman, Naotake Ogasawara, Taku Oshima, and Shu Ishikawa
  • Journal Title: DNA research Volume: なし
  • Peer Reviewed
• [Journal Article] Digital Gene Expression Profiling by 5′-End Sequencing of cDNAs during Reprogramming in the MossPhyscomitrella patens (2012)
  • Author(s): Tomoaki Nishiyama, Kaori Miyawaki, Masumi Ohshima, Kari Thompson, Akitomo Nagashima, Mitsuyasu Hasebe, and Tetsuya Kurata
  • Journal Title: PLoS ONE Volume: 7
  • Peer Reviewed
• [Journal Article] FLC : A Hidden Polycomb Response Element Shows Up Silence (2011)
  • Author(s): Buzas, D., Tamada, Y., Kurata, T.
  • Journal Title: Plant and Cell Physiology Volume: (オンライン) Issue: 5 Pages: 20-20
  • DOI: 10.1093/pcp/pcr163
  • Peer Reviewed / Open Access
• [Presentation] Coordinated leaf growth through the action of sister Zn-finger transcription factors in Arabidopsis (2014)
  • Author(s): Tetsuya Kurata
  • Organizer: 日本植物生理学会
  • Place of Presentation: 富山大学
• [Presentation] シロイヌナズナの器官成長に必要なZnフィンガー転写因子の解析 (2013)
  • Author(s): 倉田 哲也、大島 真澄
  • Organizer: 日本植物学会
  • Place of Presentation: 北海道大学
• [Presentation] NAISTにおける植物科学グローバルトップ教育推進プログラム
  • Author(s): 倉田哲也, 稲田のりこ, 深尾陽一朗, 藤原正幸, 梅田正明, 田坂昌生, 島本功
  • Organizer: 日本植物生理学会
  • Place of Presentation: 岡山大学
• [Book] Arabidopsis Protocols (2014)
  • Author(s): Naoyuki Uchida, Tomoaki Sakamoto, Masao Tasaka and Tetsuya Kurata
  • Total Pages: 11
  • Publisher: Humana Press
• [Remarks] 植物グローバル教育プロジェクト、ゲノム・トランスクリプトームグループ
  • URL: http://bsw3.naist.jp/plantglobal/team/genome/index.shtml