Understanding biological ignificance of histone modifications by epigenetic manipulation using multifunctional antibodies

• Project/Area Number: 26291071
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Genetics/Chromosome dynamics
• Research Institution: Tokyo Institute of Technology
• Principal Investigator: Kimura Hiroshi 東京工業大学, 科学技術創成研究院, 教授 (30241392)
• Project Period (FY): 2014-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥15,860,000 (Direct Cost: ¥12,200,000、Indirect Cost: ¥3,660,000); Fiscal Year 2016: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2015: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2014: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
• Keywords: クロマチン / エピジェネティクス / 遺伝子発現制御 / 転写 / ヒストン修飾 / 細胞分裂 / 抗体 / 遺伝子 / 細胞・組織 / バイオテクノロジー / シグナル伝達 / ゲノム / エピジェネティクス制御 / 染色体

Outline of Final Research Achievements

DNA in eukaryotic nuclei forms chromatin by binding with histone proteins. Histones are subjected to a variety of posttranslational modifications, but the biological significance of those modifications remains largely unknown. In this study, we performed inhibitory assay based on antibody injection, identification of proteins that bind to specifically modified chromatin, and development of new live cell modification probes. When phosphorylated histone-specific probes were injected into cells, chromosome missegregation was observed, which probably resulted from bridging between sister chromatids. A candidate protein that bound to phsophorylated chromatin localized to centromeres. Finally, we developed some new modification-specific intracellular antibody probes that could monitor specific modifications in living cells.

Research Products

• [Int'l Joint Research] キュリー研究所/ツールーズ大学(フランス)
• [Int'l Joint Research] フロリダ州立大学/ロックフェラー大学(米国)
• [Int'l Joint Research] エジンバラ大学(英国)
• [Int'l Joint Research] Curie Institute/University of Toulouse(フランス)
• [Int'l Joint Research] University of Edinburgh(英国)
• [Int'l Joint Research] University of Edinbrough(英国)
• [Int'l Joint Research] Max Delbruck Center(ドイツ)
• [Journal Article] NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence (2018)
  • Author(s): Parry AJ, Hoare M, Bihary D, Hansel-Hertsch R, Smith S, Tomimatsu K, Mannion E, Smith A, D'Santos P, Russel IA, Balasubramanian S, Kimura H, Samarajiwa SA, Narita M.
  • Journal Title: Nature Communications Volume: 9 Pages: 1840-1840
  • DOI: 10.1038/s41467-018-04283-9
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] HP1α targets the chromosomal passenger complex for activation at heterochromatin before mitotic entry. (2018)
  • Author(s): Ruppert JG, Samejima K, Platani M, Molina O, Kimura H, Jeyaprakash AA, Ohta S, Earnshaw WC.
  • Journal Title: The EMBO Journal Volume: 37
  • DOI: 10.15252/embj.201797677
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] HELLS and CDCA7 comprise a bipartite nucleosome remodeling complex defective in ICF syndrome. (2018)
  • Author(s): Jenness C, Giunta S, Muller MM, Kimura H, Muir TW, Funabiki H.
  • Journal Title: Proc Natl Acad Sci USA Volume: 115
  • DOI: 10.1073/pnas.1717509115
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2. (2018)
  • Author(s): Chen CCL, Goyal P, Karimi MM, Abildgaard MH, Kimura H, Lorincz MC.
  • Journal Title: Genome Res Volume: 28 Pages: 37-51
  • DOI: 10.1101/gr.224717.117
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Nucleosome stability measured in situ by automated quantitative imaging (2017)
  • Author(s): Imre L, Simandi Z, Horvath A, Fenyofalvi G, Nanasi P, Niaki EF, Hegedus E, Bacso Z, Weyemi U, Mauser R, Ausio J, Jeltsch A, Bonner W, Nagy L, Kimura H, Szabo G.
  • Journal Title: Sci Rep Volume: 7 Pages: 12743-12743
  • DOI: 10.1038/s41598-017-12608-9
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Semi-quantitative Analysis of H4K20mel Levels in Living Cells Using Mintbody (2017)
  • Author(s): Sato Y, Kimura H
  • Journal Title: Bio-protocol Volume: 7
  • DOI: 10.21769/bioprotoc.2276
  • Peer Reviewed / Open Access
• [Journal Article] 3. Global histone modification fingerprinting in human cells using epigenetic reverse phase protein array (2017)
  • Author(s): Partolina M, Thoms HC, MacLeod KG, Rodriguez-Blanco G, Clarke MN, Venkatasubramani AV, Beesoo R, Larionov V, Neergheen-Bhujun VS, Serrels B, Kimura H, Carragher NO, Kagansky A.
  • Journal Title: Cell Death Discov Volume: 3 Pages: 16077-16077
  • DOI: 10.1038/cddiscovery.2016.77
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] A genetically encoded probe for live-cell imaging of H4K20 monomethylation (2017)
  • Author(s): Sato Y., Kujirai T., Arai R., Asakawa H., Ohtsuki C., Horikoshi N., Yamagata K., Ueda J., Nagase T., Haraguchi T., Hiraoka Y., Kimura A., Kurumizaka H., Kimura, H.
  • Journal Title: Jouenal of Molecular Biology Volume: 428 Pages: 3885-3902
  • DOI: 10.1016/j.jmb.2016.08.010
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Nucleome研究の世界動向 (2017)
  • Author(s): 田代 聡、木村 宏
  • Journal Title: 実験医学 Volume: 35 Pages: 78-82
• [Journal Article] Histone H4 lysine 20 acetylation is associated with gene repression in human cells. (2016)
  • Author(s): Kaimori, J. Y., Maehara, K., Hayashi-Takanaka, Y., Harada, A., Fukuda, M., Yamamoto, S., Ichimaru, N., Umehara, T., Yokoyama, S., Matsuda, R., Ikura, T., Nagao, K., Obuse, C., Nozaki, N., Takahara, S., Takao, T., Ohkawa, Y., Kimura, H., and Isaka, Y.
  • Journal Title: Scientific Reports Volume: 6 Pages: 24318-24318
  • DOI: 10.1038/srep24318
  • NAID: 120005770760
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] エピゲノム解析手法の標準化：ヒストン修飾解析 (2016)
  • Author(s): 木村 宏
  • Journal Title: 実験医学増刊『エピゲノム研究：修飾の全体像の理解から先制・個別化医療へ』 Volume: 34 Pages: 32-37
• [Journal Article] Epigenetic engineering shows that a human centromere resists silencing mediated by H3K27me3/K9me3. (2016)
  • Author(s): Martins NMC, Bergmann JH, Shono N, Kimura H, Larionov V, Masumoto H and Earnshaw WC.
  • Journal Title: Mol Biol Cell Volume: 27 Pages: 177-196
  • DOI: 10.1091/mbc.e15-08-0605
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells. (2015)
  • Author(s): Dias JD, Rito T, Torlai Triglia E, Kukalev A, Ferrai C, Chotalia M, Brookes E, Kimura H, Pombo A
  • Journal Title: eLIFE Volume: 4
  • DOI: 10.7554/elife.11215
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] CENP-C and CENP-I are key connecting factors for kinetochore and CENP-A assembly. (2015)
  • Author(s): Shono N, Ohzeki J, Otake K, Martins NMC, Nagase T, Kimura H, Larionov V, Earnshaw WC, Masumoto H.
  • Journal Title: J Cell Sci Volume: 128 Pages: 4572-4587
  • DOI: 10.1242/jcs.180786
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Distribution of histone H4 modifications as revealed by a panel of specific monoclonal antibodies. (2015)
  • Author(s): Hayashi-Takanaka Y., Maehara K., Harada A., Umehara T., Yokoyama S., Obuse C., Ohkawa Y., Nozaki N., Kimura H.
  • Journal Title: Chromosome Res Volume: 23 Pages: 735-766
  • DOI: 10.1007/s10577-015-9486-4
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] Chromatin modification dynamics during gene activation in living cells (2017)
  • Author(s): 木村宏
  • Organizer: 4D Nucleome : The Cell Nucleus in Space and Time
  • Int'l Joint Research / Invited
• [Presentation] Chromatin modification dynamics during gene activation in living cells (2017)
  • Author(s): 木村宏
  • Organizer: 10th Berlin Summer Meeting
  • Int'l Joint Research / Invited
• [Presentation] Chromatin modification dynamics during cell differentiation (2017)
  • Author(s): 木村宏
  • Organizer: Gordon Research Conference “Genome Architecture in Cell Fate & Disease”
  • Int'l Joint Research / Invited
• [Presentation] Chromatin modification dynamics during cell differentiation (2017)
  • Author(s): 木村宏
  • Organizer: HMGU-Japan Epigenetics and Chromatin Meeting
  • Int'l Joint Research / Invited
• [Presentation] Chromatin Integration Labeling Technology (2017)
  • Author(s): 木村宏
  • Organizer: 平成29年度遺伝研研究会『エピジェネティクスの基盤となるクロマチン・細胞核の動的構造変換』
  • Invited
• [Presentation] クロマチン修飾ダイナミクスと転写制御 (2017)
  • Author(s): 木村宏
  • Organizer: 第40回日本分子生物学会年会
  • Invited
• [Presentation] クロマチン修飾動態解析によるクレオーム研究 (2017)
  • Author(s): 木村 宏
  • Organizer: よこはまMNR研究会主催 第56回ワークショップ
  • Place of Presentation: 横浜市
  • Invited
• [Presentation] Live cell imaging of histone and RNA polymerase II modifications (2016)
  • Author(s): Hiroshi Kimura
  • Organizer: 第39回 日本分子生物学会年会シンポジウム『ヌクレオーム研究の幕開け』
  • Place of Presentation: 横浜市
  • Year and Date: 2016-11-30
  • Invited
• [Presentation] 転写活性化におけるヒストン修飾の役割 (2016)
  • Author(s): 木村 宏
  • Organizer: 遺伝研研究会『クロマチン・細胞核の動的構造変換とエピジェネティクス制御
  • Place of Presentation: 三島市
  • Year and Date: 2016-10-27
  • Invited
• [Presentation] Visualizing protein modifications in vivo (2016)
  • Author(s): 木村 宏
  • Organizer: 新学術領域研究『環境記憶統合』第２回若手の会
  • Place of Presentation: 熱海市
  • Year and Date: 2016-10-13
  • Invited
• [Presentation] Tracking posttranslational and epigenetic modifications of endogenous proteins in vivo (2015)
  • Author(s): Hiroshi Kimura
  • Organizer: 24th Wilhelm Bernhard Workshop on the Cell Nucleus/57th Symposium of the Society for Histochemistry
  • Place of Presentation: Schloss Wilhelminenberg, Vienna, Austria
  • Year and Date: 2015-08-20
  • Int'l Joint Research / Invited
• [Presentation] エピゲノム修飾の生細胞・生体内ダイナミクス (2015)
  • Author(s): 木村 宏
  • Organizer: 第9回日本エピジェネティクス研究会
  • Place of Presentation: 学術総合センター
  • Year and Date: 2015-05-25
  • Invited
• [Remarks] 木村宏 研究室
  • URL: http://kimura-lab.bio.titech.ac.jp/index.html
• [Remarks] 東工大 木村宏 研究者情報
  • URL: http://t2r2.star.titech.ac.jp/cgi-bin/researcherinfo.cgi?q_researcher_content_number=CTT100673940#
• [Remarks] 東工大 細胞制御工学研究センター
  • URL: http://www.rcb.iir.titech.ac.jp/
• [Remarks] 東京工業大学 木村研究室
  • URL: http://kimura-lab.bio.titech.ac.jp/
• [Remarks] 東京工業大学 科学技術創成研究院 細胞制御工学研究センター
  • URL: http://cell-biology.jimdo.com/
• [Remarks] 東京工業大学 リサーチリポジトリ 木村宏
  • URL: http://t2r2.star.titech.ac.jp/cgi-bin/researcherinfo.cgi?q_researcher_content_number=CTT100673940
• [Remarks] 東京工業大学 木村宏研究室
  • URL: http://kimura-lab.bio.titech.ac.jp/
• [Remarks] 東京工業大学 科学技術創成研究院 細胞制御工学ユニット
  • URL: http://cell-biology.jimdo.com/
• [Remarks] 東京工業大学 生命理工学研究科 木村研究室
  • URL: http://www.bio.titech.ac.jp/laboratory/kimura-kajikawa/kimura/index.html
• [Patent(Industrial Property Rights)] ヒストンH3トリメチル化リシン特異的モノクローナル抗体又はその抗原結合性断片 (2017)
  • Inventor(s): 木村 宏、佐藤優子、大井彰人、胡桃坂仁志、鯨井智也、他
  • Industrial Property Rights Holder: 東京工業大学
  • Industrial Property Rights Type: 特許
  • Industrial Property Number: 2017-111580
  • Filing Date: 2017