Simultaneous imaging of chromatin fractal dimensions and temperature in living cell nucleus

• Project/Area Number: 16K14655
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: System genome science
• Research Institution: Institute of Physical and Chemical Research (2017); Hiroshima University (2016)
• Principal Investigator: Shinkai Soya 国立研究開発法人理化学研究所, 生命システム研究センター, 研究員 (60547058)
• Co-Investigator(Kenkyū-buntansha): 菅原 武志 広島大学, 理学研究科, 特任助教 (60713005)
• Co-Investigator(Renkei-kenkyūsha): OKABE Kohki 東京大学, 薬学系研究科, 助教 (20455398) ; OCHIAI Hiroshi 広島大学, 理学研究科, 特任講師 (60640753)
• Research Collaborator: TAKEDA Shunsuke
• Project Period (FY): 2016-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000); Fiscal Year 2017: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2016: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: クロマチン構造 / フラクタル次元 / 蛍光寿命イメージング / 染色体構造 / 温度イメージング

Outline of Final Research Achievements

Each human cell contains total 2 meter of genomic DNA in a cell nucleus with a 10-micro-meter diameter. How chromatin fibers spatially condense is unclear. In this study, we tried to spatially quantify fractal dimensions, which are mathematical barometers for any structures, of chromatin fibers in living cells. The method is based on energy transfer between two fluorescent probes on fractal structures. The efficiency depends on fractal dimensions. Therefore, we made cells with two fluorescent probes on chromatin fibers. Finally, we developed an imaging method to spatially quantify fractal dimensions of chromatin fibers.

Research Products

• [Journal Article] Bridging the dynamics and organization of chromatin domains by mathematical modeling (2017)
  • Author(s): Shinkai S, Nozaki T, Maeshima K, Togashi Y
  • Journal Title: Nucleus Volume: 印刷中 Issue: 4 Pages: 353-359
  • DOI: 10.1080/19491034.2017.1313937
  • Peer Reviewed / Open Access
• [Journal Article] Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells (2016)
  • Author(s): Shinkai S, Nozaki T, Maeshima K, Togashi Y
  • Journal Title: PLoS Comput Biol Volume: 12 Issue: 10 Pages: e1005136-e1005136
  • DOI: 10.1371/journal.pcbi.1005136
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] クロマチン動態と構造をつなぐ数理 (2017)
  • Author(s): 新海創也
  • Organizer: 生命動態の分子メカニズムと数理
  • Place of Presentation: 理研QBiC（大阪府）
  • Year and Date: 2017-03-17
  • Invited
• [Presentation] Bridging the dynamics and organization of chromatin domains by mathematical modeling (2017)
  • Author(s): Soya Shinkai
  • Organizer: 5th International Symposium of the Mathematics on Chromatin Live Dynamics
  • Place of Presentation: 東広島
  • Year and Date: 2017-03-07
  • Int'l Joint Research
• [Presentation] 数理で解き明かすクロマチン動態と構造の関係 (2017)
  • Author(s): 新海創也
  • Organizer: 理研公開シンポジウム「観る・測る・ 解く」 4 次元細胞計測の現状と未来
• [Presentation] Bridging the gap between th dynamics and organization of chromatin domains by mathematical modeling (2017)
  • Author(s): Soya Shinkai
  • Organizer: Taiwan-Japan Joint Meeting on Bioimaging for Young researchers -Resonance Bio - Academia Sinica - 4D Cell -
  • Int'l Joint Research
• [Presentation] 細胞内温度を記述する術を我々は手にしているか？ (2016)
  • Author(s): 新海創也
  • Organizer: 第1 回Biothermology Workshop
  • Place of Presentation: 基礎生物学研究所（岡崎市）
  • Year and Date: 2016-12-10
  • Invited
• [Presentation] Dynamic nucleosome movement provides structural information of topological chromatin domains in living human cells (2016)
  • Author(s): Soya Shinkai, Tadasu Nozaki, Kazuhiro Maeshima, Yuichi Togashi
  • Organizer: 2016 Workshop on DNA Reactions and DNA/Chromosome Dynamics
  • Place of Presentation: Marine Biological Laboratory, USA
  • Year and Date: 2016-09-11
  • Int'l Joint Research
• [Presentation] 核内クロマチン動態とクロマチンドメイン構造をつなぐモデルのデザインと実験との融合 (2016)
  • Author(s): 新海創也, 野崎慎, 前島一博, 冨樫祐一
  • Organizer: CREST「生命動態の理解と制御のための基盤技術の創出」研究領域第6回数理デザイン道場
  • Place of Presentation: 三島
  • Year and Date: 2016-06-13
• [Presentation] 染色体の動的階層性 (2016)
  • Author(s): 新海創也
  • Organizer: 細胞システムの動態と論理VIII
  • Place of Presentation: 理化学研究所（和光市）
  • Year and Date: 2016-04-14
  • Invited