Analysis of DNA methylation in the reproductive cells using a tiling array

• Project/Area Number: 19380004
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Breeding science
• Research Institution: The University of Tokyo
• Principal Investigator: NAKAZONO Mikio The University of Tokyo, 大学院・農学生命科学研究科, 准教授 (70282697)
• Co-Investigator(Kenkyū-buntansha): 堤 伸浩 東京大学, 大学院・農学生命科学研究科, 教授 (00202185) ; 木下 哲 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 (60342630) ; 石丸 努 独立行政法人農業食品産業技術総合研究機構, 作物研究所, 任期付研究員 (40414635)
• Co-Investigator(Renkei-kenkyūsha): TSUTSUMI Nobuhiro 東京大学, 大学院・農学生命科学研究科, 教授 (00202185) ; KINOSHITA Tetsu 奈良先端科学技術大学, 大学院・バイオサイエンス研究科, 准教授 (60342630) ; ISHIMARU Tsutomu 独立行政法人農業食品産業技術総合研究機構, 作物研究所, 研究員 (40414635)
• Project Period (FY): 2007 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥20,410,000 (Direct Cost: ¥15,700,000、Indirect Cost: ¥4,710,000); Fiscal Year 2009: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000); Fiscal Year 2008: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000); Fiscal Year 2007: ¥9,620,000 (Direct Cost: ¥7,400,000、Indirect Cost: ¥2,220,000)
• Keywords: レーザーマイクロダイセクション / DNAメチレーション / イネ / 生殖系列 / DNAメチル化 / タイリングアレイ / LMD

Research Abstract

In this research, we tried to investigate DNA methylation pattern in laser microdissection (LMD)-isolated embryo and endosperm by a tiling array. We examined optimal conditions for bisulfite sequencing using total DNA extracted from some tissues in rice. We succeeded in the bisulfite sequencing when we used enough amounts of DNA, but failed in the sequencing using small amounts of DNA extracted from the LMD isolated tissues. As a result, we did not succeed in solution of this problem, and thus were not able to carry out the tiling array. We are continuing to examine the optimal conditions for the bisulfite sequencing using small amounts of DNA.

Research Products

• [Journal Article] A method for obtaining high quality RNA from paraffin sections of plant tissues by laser microdissection. (2010)
  • Author(s): Takahashi, et al.
  • Journal Title: J.Plant Res. (印刷中)
  • Peer Reviewed
• [Journal Article] Formation of grain chalkiness and changes in water distribution in developing rice caryopses grown under high-temperature stress. (2009)
  • Author(s): Ishimaru, T., A.K.Horigane, M.Ida, N.Iwasawa, Y.A.San-oh, M.Nakazono, N.K.Nishizawa, T.Masumura, M.Kondo, M.Yoshida
  • Journal Title: J.Cereal Sci. 50 Pages: 166-174
• [Journal Article] Arabidopsis dynamin-related proteins DRP3A and DRP3B are functionally redundant in mitochondrial fission but have distinct roles in peroxisomal fission. (2009)
  • Author(s): Fujimoto, M., S.Arimura, S.Mane, M.Kondo, C.Saito, T.Ueda, M.Nakazono, A.Nakano, M.Nishimura, T.Tsutsumi
  • Journal Title: Plant J. 58 Pages: 388-400
• [Journal Article] Nod factor, nitrate-induced CLE genes that drive systemic regulation of nodulation. (2009)
  • Author(s): Okamoto, S., E.Ohnishi, S.Sato, H.Takahashi, M.Nakazono, S.Tabata, M.Kawaguchi
  • Journal Title: Plant Cell Physiol. 50 Pages: 67-77
• [Journal Article] Rice OsYSL15 is an iron-regulated iron(III)-deoxymugineic acid transporter expressed in the roots and is essential for iron uptake in early growth of the seedlings. (2009)
  • Author(s): Inoue, H., T.Kobayashi, T.Nozoye, M.Takahashi, Y.Kakei, K.Suzuki, M.Nakazono, H.Nakanishi, S.Mori, N.K.Nishizawa
  • Journal Title: J.Biol.Chem. 284 Pages: 3470-3479
• [Journal Article] Formation of grain chalkiness and changes in water distribution in developing rice caryopses grown under high-temperature stress. (2009)
  • Author(s): Ishimaru, et al.
  • Journal Title: J.Cereal Sci. 50 Pages: 166-174
  • Peer Reviewed
• [Journal Article] Nod factor, nitrate-induced CLE genes that drive systemic regulation of nodulation. (2009)
  • Author(s): Okamoto, et al.
  • Journal Title: Plant Cell Physiol. 50 Pages: 67-77
  • Peer Reviewed
• [Journal Article] Rice OsYSL15 is an iron-regulated iron(III)-deoxymugineic acid transporter expressed in the roots and is essential for iron uptake in early growth of the seedlings. (2009)
  • Author(s): Inoue et al.
  • Journal Title: J. Biol. Chem. 284 Pages: 3470-3479
  • Peer Reviewed
• [Journal Article] Various spatiotemporal expression profiles of anther-expressed genes in rice. (2008)
  • Author(s): Hobo, T., K.Suwabe, K.Aya, G.Suzuki, K.Yano, T.Ishimizu, M.Fujita, S.Kikuchi, K.Hamada, M.Miyano, T.Fujioka, F.Kaneko, T.Kazama, Y.Mizuta, H.Takahashi, K.Shiono, M.Nakazono, N.Tsutsumi, Y.Nagamura, N.Kurata, M.Watanabe, M.Matsuoka
  • Journal Title: Plant Cell Physiol. 49 Pages: 1417-1428
  • NAID: 10027333889
• [Journal Article] Separated transcriptomes of male gametophyte and tapetum in rice : validity of a laser microdissection (LM) microarray. (2008)
  • Author(s): Suwabe, K., G.Suzuki, H.Takahashi, K.Shiono, M.Endo, K.Yano, M.Fujita, H.Masuko, H.Saito, T.Fujioka, F.Kaneko, T.Kazama, Y.Mizuta, M.Kawagishi-Kobayashi, N.Tsutsumi, N.Kurata, M.Nakazono, M.Watanabe
  • Journal Title: Plant Cell Physiol. 49 Pages: 1407-1416
  • NAID: 10027333829
• [Journal Article] Arabidopsis dynamin-related protein DRP2B is co-localized with DRP1A on the leading edge of the forming cell plate. (2008)
  • Author(s): Fujimoto, M., S.Arimura, M.Nakazono, N.Tsutsumi
  • Journal Title: Plant Cell Rep. 27 Pages: 1581-1586
• [Journal Article] Drought induction of Arabidopsis 9-cis-epoxycarotenoid dioxygenase occurs in vascular parenchyma cells. (2008)
  • Author(s): Endo, A., Y.Sawada, H.Takahashi, M.Okamoto, K.Ikegami, H.Koiwai, M.Seo, T.Toyomasu, W.Mitsuhashi, K.Shinozaki, M.Nakazono, Y.Kamiya, T.Koshiba, E.Nambara
  • Journal Title: Plant Physiol. 147 Pages: 1984-1993
• [Journal Article] Arabidopsis ELM1 is required for the localization of dynamin-related protein DRP3A to mitochondrial fission sites. (2008)
  • Author(s): Arimura, S., M.Fujimoto, Y.Doniwa, N.Kadoya, M.Nakazono, W.Sakamoto, N.Tsutsumi
  • Journal Title: Plant Cell. 20 Pages: 1555-1566
• [Journal Article] Role of ethylene in acclimations to promote oxygen transport in roots of plants in waterlogged soils. (2008)
  • Author(s): Shiono, K., H.Takahashi, T.D.Colmer, M.Nakazono
  • Journal Title: Plant Sci. 175 Pages: 52-58
• [Journal Article] Separated transcriptomes of male gametophyte and tapetum in rice:validity of a laser microdissection (LM) microarray. (2008)
  • Author(s): Suwabe et al.
  • Journal Title: Plant Cell Physiol. 49 Pages: 1407-1416
  • Peer Reviewed
• [Journal Article] Various spatiotemporal expression profiles of anther-expressed genes in rice. (2008)
  • Author(s): Hobo et al.
  • Journal Title: Plant Cell Physiol. 49 Pages: 1417-1428
  • Peer Reviewed
• [Journal Article] Role of ethylene in acclimations to promote oxygen transport in roots of plants in waterlogged soils (2008)
  • Author(s): Shiono, et. al.
  • Journal Title: Plant Science (掲載確定)
  • Peer Reviewed
• [Journal Article] A method for obtaining high integrity RNA from developing aleurone cells and starchy endosperm in rice (Oryza saliva L.) by laser microdissection. (2007)
  • Author(s): Ishimaru, T., M.Nakazono, T.Masumura, M.Abiko, Y.San-oh, N.K.Nishizawa, M.Kondo
  • Journal Title: Plant Sci. 173 Pages: 321-326
• [Journal Article] Rice tillering dwarf mutant dwarf3 has increased leaf longevity during darkness-induced senescence or hydrogen peroxide-induced cell death. (2007)
  • Author(s): Yan, H., H.Saika, M.Maekawa, I.Takamure, N.Tsutsumi, J.Kyozuka, M.Nakazono
  • Journal Title: Genes Genet.Syst. 82 Pages: 361-366
  • NAID: 10024394884
• [Journal Article] Ethylene promotes submergence-induced expression of OsABA8oxl, a gene that encodes ABA 8'-hydroxylase in rice. (2007)
  • Author(s): Saika, H., M.Okamoto, K.Miyoshi, T.Kushiro, S.Shinoda, Y.Jikumaru, M.Fujimoto, T.Arikawa, H.Takahashi, M.Ando, S.Arimura, A.Miyao, H.Hirochika, Y.Kamiya, N.Tsutsumi, E.Nambara, M.Nakazono
  • Journal Title: Plant Cell Physiol. 48 Pages: 287-298
• [Journal Article] Cell type-specific gene expression profiling in plants by using a combination of laser microdissection and high-throughput technologies. (2007)
  • Author(s): Ohtsu, K., H.Takahashi, P.S.Schnable, M.Nakazono
  • Journal Title: Plant Cell Physiol. 48 Pages: 3-7
  • NAID: 10018519953
• [Journal Article] Cell type-specific gene expression profiling in plants by using a combination of laser microdissection and high-throughput teclinologies (2007)
  • Author(s): Ohtsu, et. al.
  • Journal Title: Plant & Cell Physiology 48 Pages: 3-7
  • Peer Reviewed
• [Journal Article] Ethylene promotes submergence-induced expression of OsABA8oxl,a gene that encodes ABA8'-hydroxylase in rice (2007)
  • Author(s): Saika, et. al.
  • Journal Title: Plant & Cell PhySiology 48 Pages: 287-298
  • Peer Reviewed
• [Presentation] レーザーマイクロダイセクションを植物生理学に応用する (2009)
  • Author(s): 中園幹生
  • Organizer: 第50回日本植物生理学会年会
  • Place of Presentation: 名古屋
• [Presentation] イネreduced adh activity (rad)変異体の子葉鞘における細胞分裂・伸長の抑制 (2009)
  • Author(s): 高橋宏和、雑賀啓明、松村英生、長村吉晃、西澤直子、堤伸浩、中園幹生
  • Organizer: 第115回日本育種学会講演会
  • Place of Presentation: つくば.
• [Presentation] Suppression of cell division and elongation in coleoptiles of rice reduced adh activity (rad) mutant. (2009)
  • Author(s): 高橋宏和、雑賀啓明、松村英生、長村吉晃、西澤直子、堤伸浩、中園幹生
  • Organizer: Plant Biology 2009
  • Place of Presentation: Hawai, USA.
• [Presentation] Identification of genes expressed during aerenchyma formation in maize roots using laser microdissection and a microarray. (2009)
  • Author(s): 中園幹生, Imene Rajhi, 高橋宏和, 塩野克宏, Kazuhiro Ohtsu, 堤伸浩, Tieming Ji, Daniel S.Nettleton, Patrick S.Schnable, 西澤直子
  • Organizer: 7th ISRR Symposium.
  • Place of Presentation: Vienna, Austria.
• [Presentation] イネの湛水条件下における養水分吸収機構の動態 (2008)
  • Author(s): 高橋宏和、塩野克宏、長村吉晃、堤伸浩、中園幹生
  • Organizer: 第113回日本育種学会講演会
  • Place of Presentation: 川崎
• [Presentation] Identification of genes expressed during aerenchyma formation in maize roots using laser microdissection and a microarray. (2007)
  • Author(s): Nakazono, et. al.
  • Organizer: Identification of genes expressed during aerenchyma formation in maize roots using laser microdissection and a microarray.
  • Place of Presentation: Matsushima,Japan
  • Year and Date: 2007-11-23