Functional analysis of mouse noncoding RNAs by a rapid gene disruption method

• Project/Area Number: 22310118
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Genome biology
• Research Institution: Nara Medical University (2012-2013); Osaka University (2010-2011)
• Principal Investigator: HORIE Kyoji 奈良県立医科大学, 医学部, 教授 (30333446)
• Project Period (FY): 2010-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥19,630,000 (Direct Cost: ¥15,100,000、Indirect Cost: ¥4,530,000); Fiscal Year 2013: ¥9,490,000 (Direct Cost: ¥7,300,000、Indirect Cost: ¥2,190,000); Fiscal Year 2012: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000); Fiscal Year 2011: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000); Fiscal Year 2010: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
• Keywords: ES細胞 / ゲノム / 遺伝子 / non-coding RNA / 変異体 / non-oding RNA

Outline of Final Research Achievements

Recent researches demonstrated that most regions of the mammalian genome such as human and mouse are transcribed. Furthermore, most of such transcripts are noncoding RNAs. However, speculation of the function of noncoding RNAs from nucleotide sequences is difficult. We recently developed a method to rapidly generate mutant mouse ES cells. In the present study, we generated mutant mouse ES cell lines using this method and conducted systematic functional analysis of noncoding RNAs.

Research Products

• [Journal Article] Simulation and estimation of gene number in a biological pathway using almost complete saturation mutagenesis screening of haploid mouse cells (2014)
  • Author(s): Tokunaga M, Kokubu C, Maeda Y, Sese J, Horie K, Sugimoto N, Kinoshita T, Yusa K, Takeda J.
  • Journal Title: BMC Genomics Volume: 15 Issue: 1 Pages: 1016-1016
  • DOI: 10.1186/1471-2164-15-1016
  • Peer Reviewed / Open Access
• [Journal Article] Removal of reprogramming transgenes improves the tissue reconstitution potential of keratinocytes generated from human induced pluripotent stem cells (2014)
  • Author(s): Ken Igawaa, Chikara Kokubu, Kosuke Yusa, Kyoji Horie, Yasuhide Yoshimura, Kaori Yamauchi, Hirofumi Suemori, Hiroo Yokozeki, Masashi Toyoda, Nobutaka Kiyokawa, Hajime Okita, Yoshitaka Miyagawa, Hidenori Akutsu, Akihiro Umezawa, Ichiro Katayama, Junji Takeda.
  • Journal Title: Stem Cells Transl Med Volume: 3 Issue: 9 Pages: 992-1001
  • DOI: 10.5966/sctm.2013-0179
  • Peer Reviewed / Open Access
• [Journal Article] An in vitro ES cell-based clock recapitulation assay model identifies CK2a as an endogenous clock regulator (2013)
  • Author(s): Umemura Y, Yoshida J, Wada M, Tsuchiya Y, Minami Y, Watanabe H, Kondoh G, Takeda J, Inokawa H, Horie K, Yagita K.
  • Journal Title: PLoS One Volume: 8 Issue: 6 Pages: e67241-e67241
  • DOI: 10.1371/journal.pone.0067241
  • Peer Reviewed / Open Access
• [Journal Article] A homozygous mutant embryonic stem cell bank applicable for phenotype-driven genetic screening (2011)
  • Author(s): Horie K.
  • Journal Title: Nature Methods Volume: 8 Issue: 12 Pages: 1071-1077
  • DOI: 10.1038/nmeth.1739
  • Peer Reviewed
• [Presentation] ホモ変異体マウスES細胞バンクを用いた包括的遺伝子機能解析 (2014)
  • Author(s): 堀江恭二、吉田純子
  • Organizer: 第37回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2014-11-25 – 2014-11-27
  • Invited
• [Presentation] Rapid identification of homozygous mutant mouse embryonic stem cell clones showing differentiation resistant or differentiation prone phenotype (2014)
  • Author(s): Junko Yoshida, Kyoji Horie
  • Organizer: Global Controls in Stem Cells
  • Place of Presentation: Biopolis, Syngapore
  • Year and Date: 2014-11-05 – 2014-11-07
• [Presentation] Live cell imaging for the analysis of cellular heterogeneity in mouse embryonic stem cell mutant clones identified by forward genetic screening (2014)
  • Author(s): Junko Yoshida, Kyoji Horie
  • Organizer: 12th Annual Meeting of International Society for Stem Cell Research
  • Place of Presentation: Vancouver, Canada
  • Year and Date: 2014-06-18 – 2014-06-21
• [Presentation] Genome-wide comparative analyses of retroviral and DNA-type transposon vector integration sites in mouse embryonic stem cells : Implication for reprogramming study (2013)
  • Author(s): Yoshida J, Horie K.
  • Organizer: 11th Annual Meeting of International Society for Stem Cell Research
  • Place of Presentation: Boston, USA
• [Presentation] レトロウィルスおよびトランスポゾンベクターのゲノムワイドな挿入部位解析 (2013)
  • Author(s): 吉田純子、竹田潤二、堀江恭二
  • Organizer: 第36回日本分子生物学会
  • Place of Presentation: 神戸
• [Presentation] Screening for critical epigenetic factors involved with the regulation of pluripotency and differentiation using a homozygous mutant mouse embryonic stem cell bank (2012)
  • Author(s): Yoshida J, Takeda J, Horie K
  • Organizer: 10th Annual Meeting of International Society for Stem Cell Research
  • Place of Presentation: Yokohama
• [Presentation] ホモ変異体ES細胞バンクを用いたマウスES細胞の多能性制御因子の遺伝学的スクリーニングとエピゲノム解析 (2012)
  • Author(s): 吉田純子、竹田潤二、堀江恭二
  • Organizer: 第35回日本分子生物学会
  • Place of Presentation: 横浜
• [Presentation] Using conditional knockout of the bloom's syndrome gene in a recessive genetic screening for novel factors involved in differentiation of mouse embryonic stem cells (2011)
  • Author(s): Yoshida J
  • Organizer: 9^<th> Annual Meeting of International Society for Stem Cell Research
  • Place of Presentation: Toronto, Canada
  • Year and Date: 2011-06-16
• [Presentation] ホモ変異体マウスES細胞バンクを用いた迅速な表現型スクリーニング
  • Author(s): 堀江恭二
  • Organizer: 理研シンポジウム
  • Place of Presentation: つくば
  • Invited
• [Remarks]
  • URL: http://www.med.osaka-u.ac.jp/pub/mr-envi/www/japanese/research/index.html