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Structural analysis of genomic regions where genetic recombination was suppressed for over million years

Research Project

Project/Area Number 20310118
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field 基礎ゲノム科学
Research InstitutionThe Institute of Physical and Chemical Research

Principal Investigator

ABE Kuniya  The Institute of Physical and Chemical Research, 動物変異動態解析技術開発チーム, チームリーダー (40240915)

Co-Investigator(Kenkyū-buntansha) OOTA Satoshi  独立行政法人理化学研究所, 情報解析技術室, 専任研究員 (30391890)
Project Period (FY) 2008 – 2010
Project Status Completed (Fiscal Year 2010)
Budget Amount *help
¥19,370,000 (Direct Cost: ¥14,900,000、Indirect Cost: ¥4,470,000)
Fiscal Year 2010: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2009: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2008: ¥8,190,000 (Direct Cost: ¥6,300,000、Indirect Cost: ¥1,890,000)
Keywordsゲノム進化 / 再編 / 染色体組換え / t-ハプロタイプ / BACライブラリー / ゲノム再編成 / ゲノム進化・再編
Research Abstract

Goal of this study is to elucidate the structure and divergence of t-haplotype genome in which genetic recombination has been suppressed for over million years. Large scale DNA rearrangements including deletions and duplications were revealed by Array-CGH method, inferring the break points of inversions associated with t-haplotypes. BAC genomic library was constructed from tw5 haplotype, and clones corresponding to the t-complex region were isolated and sequenced. Exceptionally high incidence of SNPs (single nucleotide polymorphisms) has been detected between the tw5haplotype and the standard laboratory mouse strain.

Report

(4 results)
  • 2010 Annual Research Report   Final Research Report ( PDF )
  • 2009 Annual Research Report
  • 2008 Annual Research Report
  • Research Products

    (46 results)

All 2011 2010 2009 2008 Other

All Journal Article (27 results) (of which Peer Reviewed: 27 results) Presentation (14 results) Book (1 results) Remarks (4 results)

  • [Journal Article] 表現型解析の潮流・表現型の数値化と定量解析2011

    • Author(s)
      太田聡史、阿部訓也、沼田興治
    • Journal Title

      生命科学研究の戦略:疾患モデルマウスと表現型解析

      Volume: (In press)

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A new framework for studying the isochore evolution : estimation of the equilibrium GC content based on the temporal mutation rate model.2010

    • Author(s)
      Oota S., Kawamura K., Kawai Y., Saitou N.
    • Journal Title

      Genome Biol Evol 2

      Pages: 558-571

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Highly parallel SNP genotyping reveals high-resolution landscape of mono-allelic Ube3a expression associated with locus-wide antisense transcription.2010

    • Author(s)
      Numata K., Kohama C., Abe K., Kiyosawa H.
    • Journal Title

      Nucleic Acids Res. (Epub ahead of print)

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] The X-linked imprinted gene family Fthl17 shows predominantly female expression following the two-cell stage in mouse embryos.2010

    • Author(s)
      Kobayashi S., Fujihara Y. Mise N., Kaseda K., Abe K., Ishino F., Okabe M.
    • Journal Title

      Nucleic Acids Res. (Epub ahead of print)

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Genetic variation of melatonin productivity in laboratory mice under domestication.2010

    • Author(s)
      Kasahara T., Abe K., Mekada K., Yoshiki A., Kato, T.
    • Journal Title

      Proc.Natl.Acad.Sci, USA 107

      Pages: 6412-6417

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] The X-linked imprinted gene family Fthl17 shows predominantly female expression following the two-cell stage in mouse embryos.2010

    • Author(s)
      Kobayashi S., et al.
    • Journal Title

      Nucleic Acids Res.

      Volume: 38-11 Pages: 3672-3681

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation.2010

    • Author(s)
      Chow JC., et al.
    • Journal Title

      Cell.

      Volume: 141-6 Pages: 956-969

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Genome-wide analysis of expression modes and DNA methylation status at sense-antisense transcript loci in mouse.2010

    • Author(s)
      Watanabe Y., et al.
    • Journal Title

      Genomics.

      Volume: 96-6 Pages: 333-341

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Impeding Xist expression from the active X chromosome improves mouse somatic cell nuclear transfer.2010

    • Author(s)
      Inoue K., et al.
    • Journal Title

      Science.

      Volume: 330-6003 Pages: 496-499

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Highly parallel SNP genotyping reveals high-resolution landscape of mono-allelic Ube3a expression associated with locus-wide antisense transcription.2010

    • Author(s)
      Numata K., et al.
    • Journal Title

      Nucleic Acids Res.

      Volume: (In press)

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 哺乳動物におけるミトコンドリアDNAの遺伝様式:急調分離とボトルネック効果2010

    • Author(s)
      設楽浩志、Liqin Cao、米川博通
    • Journal Title

      細胞工学

      Volume: 29-5 Pages: 461-465

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A new framework for studying the isochore evolution : estimation of the equilibrium GC content based on the temporal mutation rate model2010

    • Author(s)
      Oota, S., et al.
    • Journal Title

      Genome Biol Evol.

      Volume: 2 Pages: 558-571

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] New evidence confirms that the mitochondrial bottleneck is generated without reduction of mitochondrial DNA content in early primordial germ cells of mice.2009

    • Author(s)
      Cao L., Shitara H., Sugimoto M., Hayashi J.=I., Abe K., Yonekawa H.
    • Journal Title

      PLoS genetics 5

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Usp46, encoding a ubiquitin specific peptidase, is a quantitative trait gene regulating mouse immobile behavior in the tail suspension and forced swimming tests.2009

    • Author(s)
      Tomida S, Mamiya T, Sakamaki H, Miura M, Aosaki T,Masuda M, Niwa M, Kameyama T, Kobayashi J, Iwaki Y, Imai S, Ishikawa A, Abe K, Yoshimura T, Nabeshima T, Ebihara S
    • Journal Title

      Nature Genetics 41

      Pages: 688-695

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Genetic differences among C57BL/6 substrains.2009

    • Author(s)
      Mekada K., Abe K., Murakami A., Nakamura S., Nakata H., Moriwaki K., Obata Y., Yoshiki, A.
    • Journal Title

      Exp.Anim. 58

      Pages: 141-149

    • NAID

      10024838283

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] The mouse resources at the RIKEN BioResource Center.2009

    • Author(s)
      Yoshiki A., Ike F., Mekada K., Kitaura Y., Nakata H., Hiraiwa N., Mochida K., Ijuin M., Kadota M., Murakami A., Ogura A., Abe K., Moriwaki K., Obata Y.
    • Journal Title

      Exp.Anim. 58

      Pages: 85-96

    • NAID

      10024838089

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] A high-speed congenic strategy using first-wave male germ cells.2009

    • Author(s)
      Ogonuki N, Inoue K, Hirose M, Miura I, Mochida K, Sato T, Mise N, Mekada K, Yoshiki A, Abe K, Kurihara H, Wakana S, Ogura A
    • Journal Title

      PLoS One 4(3)(Epub 2009 Mar 31)

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Outflow tract cushions perform a critical valve-like function in the early embryonic heart requiring BMPRIA-mediated signaling in cardiac neural crest.2009

    • Author(s)
      Nomura-Kitabayashi A., Phoon K.L.C., Kishigami S., Rosenthal J., Yamauchi Y., Abe K., Yamamura K., Samtani R., Lo W.C., Mishina Y.
    • Journal Title

      Am.J.Physiol.Heart Circ.Physiol. 297

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] The mouse resources at the RIKEN BioResource Center2009

    • Author(s)
      Yoshiki, A., et.al.
    • Journal Title

      Exp.Anim. 58

      Pages: 85-96

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Genetic differences among C57BL/6 substrains2009

    • Author(s)
      Mekada, K., et.al.
    • Journal Title

      Exp.Anim. 58

      Pages: 141-149

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Usp46 is a quantitative trait gene regulating mouse immobile behavior in the tail suspension and forced swimming tests2009

    • Author(s)
      Tomida S, et.al.
    • Journal Title

      Nature Genetics 41-6

      Pages: 688-695

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Outflow tract cushions perform a critical valve-like function in the early embryonic heart requiring BMPRIA-mediated signaling in cardiac neural crest2009

    • Author(s)
      Nomura-Kitabayashi, A., et.al.
    • Journal Title

      Am J Physiol Heart Circ Physiol 297-5

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Natural antisense transcripts are co-expressed with sense mRNAs in synaptoneurosomes of adult mouse forebrain.2008

    • Author(s)
      Smalheiser N.R., Lugli G., Torvik V.I., Mise N., Ikeda R., Abe K.
    • Journal Title

      Neurosci Res. 62

      Pages: 236-239

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Differences and similarities in the developmental status of embryo- derived stem cells and primordial germ cells revealed by global expression profiling.2008

    • Author(s)
      Mise N., Fuchikami T., Sugimoto M., Kobayakawa S., Ike F., Ogawa T., Tada T., Kanaya S., Noce T., Abe K.
    • Journal Title

      Genes to cells 13

      Pages: 863-877

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Comparative expression analysis uncovers novel features of endogenous antisense transcription2008

    • Author(s)
      Okada Y., et. al.
    • Journal Title

      Hum Mol Genet. 17-11

      Pages: 1631-1640

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Differences and similarities in the developmental status of embryo-derived stem cells and primordial germ cells revealed by global expression profiling2008

    • Author(s)
      Mise, N., et. al.
    • Journal Title

      Genes to cells 13-8

      Pages: 863-77

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Large-scale production of growing oocytes from neonatal mouse ovaries

    • Author(s)
      Honda, A., et. al.
    • Journal Title

      Int. J. Dev. Biol. (in press)

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Presentation] マウスt-complex劣性致死変異の同定により見えてきたVps52の機能一哺乳類初期発生における多能性細胞の分化制御因子としての役割2010

    • Author(s)
      杉本道彦、阿部訓也
    • Organizer
      遺伝学会第82回大会
    • Place of Presentation
      札幌
    • Year and Date
      2010-09-22
    • Related Report
      2010 Annual Research Report
  • [Presentation] アイソコアの進化:新しい枠組み2010

    • Author(s)
      太田聡史
    • Organizer
      第82回日本遺伝学会大会
    • Place of Presentation
      札幌
    • Year and Date
      2010-09-21
    • Related Report
      2010 Final Research Report
  • [Presentation] アイソコアの進化:新しい枠組み2010

    • Author(s)
      太田聡史
    • Organizer
      遺伝学会第82回大会
    • Place of Presentation
      札幌
    • Year and Date
      2010-09-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] C57BL/6N系統由来のBACライブラリーの構築と日本発大型リソースの整備2009

    • Author(s)
      益崎智子、山崎孝仁, 阿部訓也
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2009-12-10
    • Related Report
      2010 Final Research Report
  • [Presentation] C57BL/6N系統由来のBACライブラリーの構築と日本発大型リソースの整備2009

    • Author(s)
      益崎智子、ほか9名
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(神奈川県横浜市)
    • Year and Date
      2009-12-10
    • Related Report
      2009 Annual Research Report
  • [Presentation] Evaluations of functional processes in live animals by in vivo imaging.2009

    • Author(s)
      Liqin CAO, Kuniya ABE
    • Organizer
      第56回日本実験動物学会総会
    • Place of Presentation
      大宮
    • Year and Date
      2009-05-16
    • Related Report
      2010 Final Research Report
  • [Presentation] Mitochondrial bottleneck is not generated by the reduction of mtDNA copy number in mouse female germline2008

    • Author(s)
      Hiroshi Shitara, et. al.
    • 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大会
    • Place of Presentation
      神戸
    • Year and Date
      2008-12-12
    • Related Report
      2008 Annual Research Report
  • [Presentation] ヒトとマウスのオーソログ遺伝子における配列相同性/発現相同性の解析2008

    • Author(s)
      村田真也, ほか5名
    • 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大会
    • Place of Presentation
      神戸
    • Year and Date
      2008-12-10
    • Related Report
      2008 Annual Research Report
  • [Presentation] 生殖細胞特異的に Venus を発現する新規TgマウスとES細胞を用いた生殖細胞発生過程の研究2008

    • Author(s)
      三瀬名丹, ほか6名
    • 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大会
    • Place of Presentation
      神戸
    • Year and Date
      2008-12-09
    • Related Report
      2008 Annual Research Report
  • [Presentation] Essential role of Nanos3 for acquisition of germ cell identity in mice2008

    • Author(s)
      Kobayakawa, S., Saga, Y., Abe K.
    • Organizer
      22nd International Mammalian Genome Conference
    • Place of Presentation
      Prague, Czech Republic
    • Year and Date
      2008-11-05
    • Related Report
      2008 Annual Research Report
  • [Presentation] In Vivo Measurement of Gene Expression, Nuclear Organization and Subcellular Organelle Dynamics in Live Animals Using a Novel Laser Scanning Microscopy System2008

    • Author(s)
      Liqin Cao
    • Organizer
      2008 World molecular Imaging Congress
    • Place of Presentation
      Nice, France
    • Year and Date
      2008-09-11
    • Related Report
      2008 Annual Research Report
  • [Presentation] "行動的絶望"を司る量的形質遺伝子の特定-リズム異常を示すCSマウスを用いて-2008

    • Author(s)
      海老原史樹文, ほか11名
    • Organizer
      日本遺伝学会第80回大会
    • Place of Presentation
      名古屋
    • Year and Date
      2008-09-04
    • Related Report
      2008 Annual Research Report
  • [Presentation] マウス亜種間の兄妹交配で生じる雑種崩壊現象の表現型解析2008

    • Author(s)
      津田薫、持田慶司、吉木淳、森脇和郎、阿部訓也
    • Organizer
      第55回日本実験動物学会総会
    • Place of Presentation
      仙台
    • Year and Date
      2008-05-15
    • Related Report
      2010 Final Research Report 2008 Annual Research Report
  • [Presentation] In vivo measurement ofgene expression, nuclear organization and subcellular organelle dynamics in live animals using a novel laser scanning microscopy system2008

    • Author(s)
      Liqin Cao, et. al.
    • Organizer
      第55回日本実験動物学会総会
    • Place of Presentation
      仙台
    • Year and Date
      2008-05-15
    • Related Report
      2008 Annual Research Report
  • [Book] 生命科学研究の戦略:疾患モデルマウスと表現型解析(表現型解析の潮流・表現型の数値化と定量解析)

    • Author(s)
      太田聡史、阿部訓也、沼田興治
    • Publisher
      中山書店(印刷中)
    • Related Report
      2010 Final Research Report
  • [Remarks] ホームページ等

    • URL

      http://www.brc.riken.jp/lab/mcd/mcd2/

    • Related Report
      2010 Final Research Report
  • [Remarks]

    • URL

      http://www.brc.riken.jp/lab/mcd/germline/index.html

    • Related Report
      2010 Annual Research Report
  • [Remarks]

    • URL

      http://www.brc.riken.jp/lab/mcd/mcd2/

    • Related Report
      2010 Annual Research Report
  • [Remarks]

    • URL

      http://www.brc.riken.jp/lab/mcd/mcd2/

    • Related Report
      2009 Annual Research Report

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Published: 2008-04-01   Modified: 2016-04-21  

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