Insertion polymorphysm of retrotransposons and diversity of theplant genome

• Project/Area Number: 19570002
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Genetics/Genome dynamics
• Research Institution: The University of Tokyo
• Principal Investigator: OHTSUBO Hisako The University of Tokyo, 分子細胞生物学研究所, 講師 (20158801)
• Co-Investigator(Kenkyū-buntansha): 田村 浩一郎 首都大学東京, 都市教養学部, 准教授 (00254144)
• Project Period (FY): 2007 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2008: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2007: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
• Keywords: トランスポゾン / 多型 / ゲノム多様化 / ゲノム構築 / 進化

Research Abstract

1. シロイヌナズナ第3染色体ペリセントロメア末端のヘテロクロマチン領域について、塩基配列の微細構造解析からLys-tRNA 合成酵素遺伝子の「重複」がまず起きたこと、「重複」したそのiso-遺伝子の分岐年代の推定から、重複がアラビドプシスゲノムの大規模再編成と同時期(50-75MYA)に起きたこと、倍加したiso-遺伝子の偽遺伝子化の年代計算から、iso-遺伝子は偽遺伝子化した後、レトロトランスポゾン、トランスポゾンの度重なる挿入によってヘテロクロマチン化したと考えられる。
2. イネのレトロトランスポゾン、RIRE7は低メチル化状態で発現が上昇するレトロトランスポゾンで、イネ染色体セントロメア領域に局在する。インド型と日本型イネ系統間で多型をしめすRIRE7-TU1について、RIRE7の両LTR 上と隣接領域のメチル化パターンを解析、RIRE7挿入の有無によって対応領域のメチル化のパターンの変化を明らかにした。

Research Products

• [Journal Article] OsRecQ1, a QDE-3 homologue in rice, isrequired for RNA silencing induced byparticle bombardment for inverted repeatDNA, but not for double-stranded RNA (2008)
  • Author(s): Chen H, Samadder PP, Tanaka Y, Ohira T,Okuizumi H, Yamaoka N, Miyao A, Hirochika H,Ohira T, suchimoto S, Ohtsubo H, NishiguchiM
  • Journal Title: Plant J 56 Pages: 274-86
• [Journal Article] New SINE families from rice,OsSN, with poly(A) at the 3' ends (2008)
  • Author(s): Tsuchimoto, S., Hirao, Y., Ohtsubo, E., and Ohtsubo, H.
  • Journal Title: Genes Genet. Syst 83 Pages: 227-236
  • NAID: 10024396176
• [Journal Article] MEGA : A biologist-centric software forevolutionary analysis of DNA and proteinsequences (2008)
  • Author(s): Kumar S, Nei M, Dudley J, and Tamura K
  • Journal Title: Briefings in Bioinformatics 9 Pages: 299-306
• [Journal Article] OsRecQ1, a QDE-3 homologue in rice, is required for RNA silencing induced by particle bombardment for inverted repeat DNA, but not for double-stranded RNA (2008)
  • Author(s): Chen H, et al.
  • Journal Title: Plant J. 56 Pages: 274-286
  • Peer Reviewed
• [Journal Article] New SINE families from rice, OsSN, with poly(A) at the 3' ends. (2008)
  • Author(s): Tsuchimoto, S. et al
  • Journal Title: Genes Ggnt. Syst. 83 Pages: 217-229
  • Peer Reviewed
• [Journal Article] New SINE families from rice, OsSN, with poly (A) at the 3' ends. (2008)
  • Author(s): Tsuchimoto, S., Hirao, Y., Ohtsubo, E., and Ohtsubo, H.
  • Journal Title: Genes Genet. Syst. 印刷確定
  • NAID: 10024396176
  • Peer Reviewed
• [Journal Article] Ricetransposable elements are characterized byvarious methylation environments in thegenome (2007)
  • Author(s): Tanaka, M., Kiyohara, A., Takasu, A., Kishima, Y., Ohtsubo, H. and Sano, Y.
  • Journal Title: BMC Genomics 8 Pages: 469-469
• [Journal Article] Phylogeneticanalysis of Oryza rufipogon strains andtheir relations to Oryza sativa strains byinsertion polymorphism of rice SINEs (2007)
  • Author(s): Xu, J.-H., Cheng C., Tsuchimoto, S., Ohtsubo, H, and Ohtsubo, E.
  • Journal Title: Genes. Gent. Syst 82 Pages: 217-229
• [Journal Article] Phylogenetic analysis of Oryza rufipogon strains and their relations to Oryza sativa strains by insertion polymorphism of rice SINEs. (2007)
  • Author(s): Xu, J.-H., Cheng, C., Tsuchimoto, S., Ohtsubo, H. and Ohtsubo, E.
  • Journal Title: Genes & Genetic Systems 82 Pages: 217-229
  • NAID: 10024394358
  • Peer Reviewed
• [Journal Article] Rice transposable elements are characterized by various methylation environments in the genome. (2007)
  • Author(s): Tanaka, M., Kiyohara, A., Takasu, A., Kishima, Y., Ohtsubo, H. and Sano, Y.
  • Journal Title: BMC Genomics 8 Pages: 469-469
  • Peer Reviewed
• [Presentation] シロイヌナズナLys-tRNA合成酵素遺伝子の倍加、偽遺伝子化、ヘテロクロマチン化 (2008)
  • Author(s): 大坪久子 他
  • Organizer: 日本遺伝学会
  • Place of Presentation: 名古屋大学
  • Year and Date: 2008-09-05
• [Presentation] シロイヌナズナLys-tRNA 合成酵素 遺伝子の重複、偽遺伝子化、ヘテロクロマチン化 (2008)
  • Author(s): 大坪久子, 田村浩一郎, 大坪栄一
  • Organizer: 日本遺伝学会第80回大会
  • Place of Presentation: 名古屋
• [Presentation] Does comparativegenomics really tell us about Darwinianselection? (2008)
  • Author(s): Tamura, K
  • Organizer: 第31回日本分子生物学会年会・第81回日本生化学会大会合同年会
  • Place of Presentation: 神戸
• [Presentation] MEGA4による分子系統解析 (2008)
  • Author(s): 田村浩一郎
  • Organizer: 日本進化学会第10回大会
  • Place of Presentation: 駒場
• [Presentation] シロイヌナズナLys-tRNA synthetase (LysRS)遺伝子の倍加・偽遺伝子化およびヘテロクロマチン化 (2007)
  • Author(s): 大坪久子・田村浩一郎*・大坪栄一
  • Organizer: BMB2007(第30回日本分子生物学会年会・第80回日本生化学会大会 合同大会)BMB2007ワークショップ4W18<ゲノムダイナミクスの制御中心としての重複DNA配列群>
  • Place of Presentation: 横浜
  • Year and Date: 2007-12-08
• [Presentation] "SINE Code" is an excellenttool for identification of Oryza species (2007)
  • Author(s): H. Ohtsubo, S. Tsuchimoto, C. Cheng, J.Xu, M.Y. Kondo, N. Kurata, T. Miyabayashi,E. Ohtsubo
  • Organizer: In OBC 5 on "Speciation and Adaptation -Ecological Genomics of Model Organisms andBeyond -
  • Place of Presentation: Okazaki
• [Presentation] アブラヤシの新規レトロトランスポゾン、Ya3ファミリーの同定と挿入多型解析 (2007)
  • Author(s): 西村啓士郎、土本 卓、大坪栄一、大坪久子
  • Organizer: 日本遺伝学会第79回大会
  • Place of Presentation: 岡山
• [Presentation] シロイヌナズナLys-tRNA synthetase 遺伝子の倍加と偽遺伝子化およびヘテロクロマチン化 (2007)
  • Author(s): 大坪久子,田村浩一郎,大坪栄一
  • Organizer: BMB2007ワークショップ4W18
  • Place of Presentation: 神戸
• [Book] Rice retroposon, p-SINE and its use for classification and identification of Oryza species In "Rice Biology in the Genomics Era" in the Series (2008)
  • Author(s): Ohtsubo, H., Tsuchimoto, S., Xu, J-X., Cheng, C., Kondo, MY., Kurata, N. and Ohtsubo. E.
  • Publisher: Biotechnology in Agriculture and Forestry, eds. A. Hirai, T. Sasaki, Y. Sano, and H. Hirano, Springer
• [Book] "Rice Biology in the Genomics Era"in the Series: Biotechnology in Agriculture and Forestry (2008)
  • Author(s): Ohtsubo, H. et al.
  • Total Pages: 381
  • Publisher: Springer, Heidelberg, Germany
• [Book] Rice retroposon, p-SINE and its use for classification and identification of Oryza species In "Rice Biology in the Genomics Era" in the Series: Biotechnology in Agriculture and Forestry (2008)
  • Author(s): Hisaka Ohtsubo, Suguru Tsuchimoto, Jian-Hong Xu, Chaoyang Cheng, Marcia Y. Kondo, Nori Kurata and Eiichi
  • Publisher: Springer, Heidelberg, Germany
• [Remarks]
  • URL: http://www.shigen.nig.ac.jp/rice/oryzabase/wild/psinecodeAbout.jsp,
• [Remarks]
  • URL: http://www.shigen.nig.ac.jp/rice/oryzabase/wild/coreCollection.jsp;jsessionid=646393DIFDBFE47D920526A3F7B31ACD.4_6,
• [Remarks]
  • URL: http://www-db.ccr.u-tokyo.ac.jplccr_usr/data/2894.html
• [Remarks]
  • URL: http://www.iam.u-tokyo.ac.jp/oh9ken/index.html
• [Remarks]
  • URL: http://www.shigen.nig.ac.jp/rice/oryzabase/wild/psinecodeAbout.jsp