Live cell imaging of histone methylation and inactive X chromosome dynamics

2013 Fiscal Year Final Research Report

• Project/Area Number: 22370063
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Molecular biology
• Research Institution: Osaka University
• Principal Investigator: KIMURA Hiroshi 大阪大学, 生命機能研究科, 准教授 (30241392)
• Project Period (FY): 2010-04-01 – 2013-03-31
• Keywords: 染色体動態 / エピジェネティクス制御 / クロマチン / ヒストン修飾 / 生細胞イメージング / 生体イメージング / 転写制御

Research Abstract

In order to visualize dynamics of inactive X chromosome, we developed two methods monitoring histone modifications in living cells. The first method uses fluorescently labeled antigen-binding fragment (Fab), which binds to endogenous modifications when loaded into living cells. Using this technique, we were able to track the behavior of inactive X chromosomes, where trimethylated histone H3K27me3 is enriched, during the cell cycle. The second method is a genetically encoded system using a single-chain variable fragment tagged with the green fluorescent protein. These methods will be useful to track epigenetic changes during development and differentiation.

Research Products

• [Journal Article] Genetically encoded system to track histone modification in vivo (2013)
  • Author(s): Sato Y, Mukai M, Ueda J, Muraki M, Stasevich TJ, Horikoshi N, Kujirai T, Kita H, Kimura T, Hira S, Okada Y, Hayashi-Takanaka Y, Obuse C, Kurumizaka H, Kawahara A, Yamagata K, Nozaki N, and Kimura H
  • Journal Title: Sci Rep Volume: 3 Pages: 2436
  • DOI: 10.1038/srep02436
  • Peer Reviewed
• [Journal Article] Histone modification for human epigenome analysis (2013)
  • Author(s): Kimura H
  • Journal Title: J Hum Genet Volume: 58 Pages: 439-445
  • DOI: 10.1038/jhg.2013.66
  • Peer Reviewed
• [Journal Article] Chromosome engineering allows the efficient isolation of vertebrate neocentromeres (2013)
  • Author(s): Shang WH, Hori T, Martins NM, Toyoda A, Misu S, Monma N, Hiratani I, Maeshima K, Ikeo K, Fujiyama A, Kimura H, Earnshaw WC, and Fukagawa T
  • Journal Title: Dev Cell Volume: 24 Pages: 635-648
  • DOI: 10.1016/j.devcel.2013.02.009
  • Peer Reviewed
• [Journal Article] Human inactive X chromosome is compacted through a PRC2-independent SMCHD1–HBiX1 pathway (2013)
  • Author(s): Nozawa RS, Nagao K, Igami K, Shibata S, Shirai N, Nozaki N, Sado T, Kimura H, and Obuse C
  • Journal Title: Nat Struct Mol Biol Volume: 20 Pages: 566-573
  • DOI: 10.1038/nsmb.2532
  • Peer Reviewed
• [Journal Article] Vertebrate Spt2 is a novel nucleolar histone chaperone that assists in ribosomal DNA transcription (2013)
  • Author(s): Osakabe A, Tachiwana H, Takaku M, Hori T, Obuse C, Kimura H, Fukagawa T, and Kurumizaka H
  • Journal Title: J Cell Sci Volume: 126 Pages: 1323-1332
  • DOI: 10.1242/jcs.112623
  • Peer Reviewed
• [Journal Article] Nap1 regulates proper CENP-B binding to nucleosomes (2013)
  • Author(s): Tachiwana H, Yuta M, Shono N, Ohzeki J-i, Osakabe A, Otake K, Larionov V, Earnshaw WC, Kimura H, Masumoto H, and Kurumizaka H
  • Journal Title: Nucleic Acids Res
  • DOI: 10.1093/nar/gks1464
  • Peer Reviewed
• [Journal Article] Predominant expression of H3K9 methyltransferases in prehypertrophic and hypertrophic chondrocytes during mouse growth plate cartilage development (2013)
  • Author(s): Ideno H, Shimada A, Imaizumi K, Kimura H, Abe M, Nakashima K, and Nifuji A
  • Journal Title: Gene Expr Pat Volume: 13 Pages: 84-90
  • DOI: 10.1016/j.gep.2013.01.002
  • Peer Reviewed
• [Journal Article] Posttranscriptional regulation of histone lysine methyltransferase GLP in embryonic male germ cell (2013)
  • Author(s): Deguchi K, Nagamatsu G, Miyachi H, Kato Y, Morita S, Kimura H, Kitano S, Hatada I, Saga Y, Tachibana M, and Shinkai Y
  • Journal Title: Biol Reprod Volume: 88 Pages: 36
  • DOI: 10.1095/biolreprod.112.103572
  • Peer Reviewed
• [Journal Article] Hinge and chromoshadow of HP1αparticipate in recognition of K9 methylated histone H3 in nucleosomes (2013)
  • Author(s): Mishima Y, Watanabe M, Kawakami T, Jayasinghe CD, Otani J, Kikugawa Y, Shirakawa M, Kimura H, Nishimura O, Aimoto S, Tajima S, and Suetake I
  • Journal Title: J Mol Biol Volume: 425 Pages: 54-70
  • DOI: 10.1016/j.jmb.2012.10.018
  • Peer Reviewed
• [Journal Article] Reliable detection of epigenetic histone marks and nuclear proteins in tissue cryosections (2012)
  • Author(s): Eberhart A, Kimura H, Leonhardt H, Joffe B, and Solovei I
  • Journal Title: Chromosome Res Volume: 20 Pages: 849-858
  • DOI: 10.1007/s10577-012-9318-8
  • Peer Reviewed
• [Journal Article] Chromosome-wide regulation of euchromatin-specific 5mC to 5hmC conversion in mouse ES cells and female human somatic cells (2012)
  • Author(s): Kubiura M, Okano M, Kimura H, Kawamura F, and Tada M
  • Journal Title: Chromosome Res Volume: 20 Pages: 837-848
  • DOI: 10.1007/s10577-012-9317-9
  • Peer Reviewed
• [Journal Article] H4K20me1 contributes to downregulation of X-linked genes for C. elegans dosage compensation (2012)
  • Author(s): Vielle A, Lang J, Dong Y, Ercan S, Kotwaliwale C, Rechtsteiner A, Appert A, Chen QB, Dose A, Egelhofer T, Kimura H, Stempor P, Dernburg A, Lieb JD, Strome S, and Ahringer J
  • Journal Title: PLoS Genet Volume: 8 Pages: e1002933
  • DOI: 10.1371/journal.pgen.1002933
  • Peer Reviewed
• [Journal Article] H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells (2012)
  • Author(s): Karmodiya K, Krebs AR, Oulad-Abdelghani M, Kimura H, and Tora L
  • Journal Title: BMC Genomics Volume: 13 Pages: 424
  • DOI: 10.1186/1471-2164-13-424
  • Peer Reviewed
• [Journal Article] Histone chaperone activity of Fanconi anemia proteins, FANCD2 and FANCI, is required for DNA crosslink repair (2012)
  • Author(s): Sato K, Ishiai M, Toda K, Furukoshi S, Osakabe A, Tachiwana H, Takizawa Y, Kagawa W, Kitao H, Dohmae N, Obuse C, Kimura H, Takata M, and Kurumizaka H
  • Journal Title: EMBO J Volume: 31 Pages: 3524-3536
  • DOI: 10.1038/emboj.2012.197
  • Peer Reviewed
• [Journal Article] Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation (2012)
  • Author(s): Chandra T, Kirschner K, Thuret JY, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T, Stark R, Janky R, Narita M, Xue L, Chicas A, Nũnez S, Janknecht R, Hayashi-Takanaka Y, Wilson MD, Marshall A, Odom DT, Babu MM, Bazett-Jones DP, Tavaré S, Edwards PA, Lowe SW, Kimura H, Gilbert DM, and Narita M
  • Journal Title: Mol Cell Volume: 47 Pages: 203-214
  • DOI: 10.1016/j.molcel.2012.06.010
  • Peer Reviewed
• [Journal Article] Breaking the HAC Barrier : Histone H3K9 acetyl/methyl balance regulates CENP-A assembly (2012)
  • Author(s): Ohzeki J-i, Bergmann JH, Kouprina N, Noskov VN, Nakano M, Kimura H, Earnshaw WC, Larionov V, and Masumoto H
  • Journal Title: EMBO J Volume: 31 Pages: 2391-2402
  • DOI: 10.1038/emboj.2012.82
  • Peer Reviewed
• [Journal Article] Roles of histone H3K9 methyltransferases during Drosophila spermatogenesis (2012)
  • Author(s): Ushijima Y, Inoue YH, Konishi T, Kitazawa D, Yoshida H, Shimaji K, Kimura H, and Yamaguchi M
  • Journal Title: Chromosome Res Volume: 20 Pages: 319-331
  • DOI: 10.1007/s10577-012-9276-1
  • Peer Reviewed
• [Journal Article] Fluorescence cell imaging and manipulation using conventional halogen lamp microscopy (2012)
  • Author(s): Yamagata K, Iwamoto D, Terashita Y, Li C, Wakayama S, Hayashi-Takanaka Y, Kimura H, Saeki K, and Wakayama T
  • Journal Title: PLoS ONE Volume: 7 Pages: e31638
  • DOI: 10.1371/journal.pone.0031638
  • Peer Reviewed
• [Journal Article] Tracking epigenetic histone modifications in single cells using Fab-based live endogenous modification labeling
  • Author(s): Hayashi-Takanaka Y, Yamagata K, Wakayama T, Stasevich TJ, Kainuma T, Tsurimoto T, Tachibana M, Shinkai Y, Kurumizaka H, Nozaki N, and Kimura H
  • Journal Title: Nucleic Acids Res Volume: 39 Pages: 6475-6488
  • DOI: 10.1093/nar/gkr343
  • Peer Reviewed
• [Presentation] ヒストン翻訳後修飾の生細胞動態可視化プローブの開発 (2012)
  • Author(s): 木村宏
  • Organizer: 第85回日本生化学会大会・シンポジウム「ヒストンの多様性とクロマチン機能制御機構」
  • Place of Presentation: 福岡
  • Year and Date: 20121214-16
  • Invited
• [Presentation] ヒストン修飾動態制御の単一細胞解析 (2012)
  • Author(s): 木村宏
  • Organizer: 第35回日本分子生物学会年会ワークショップ「細胞核構造体によるエピゲノム制御機構」
  • Place of Presentation: 福岡
  • Year and Date: 20121211-14
  • Invited
• [Presentation] Dynamic regulation of epigenetic modifications in living cells. (2012)
  • Author(s): Hiroshi Kimura
  • Organizer: The 2nd International Workshop on Structural Epigenomics
  • Place of Presentation: Yokohama, Japan
  • Year and Date: 2012-10-10
  • Invited
• [Presentation] Monitoring epigenetic modifications in living cells (2011)
  • Author(s): Hiroshi Kimura
  • Organizer: 第34回日本分子生物学会年会ワークショップ「染色体における遺伝情報の発現と維持のメカニズム」
  • Place of Presentation: 横浜
  • Year and Date: 20111213-16
  • Invited
• [Presentation] ヒストンH3のメチル化とアセチル化の生細胞ダイナミクス (2011)
  • Author(s): 木村宏
  • Organizer: 第84回日本生化学会大会シンポジウム「クロマチンダイナミクスによるエピジェネティクスの分子機構」
  • Place of Presentation: 京都
  • Year and Date: 20110921-24
  • Invited
• [Presentation] 蛋白質翻訳後修飾の生細胞イメージング (2011)
  • Author(s): 木村宏
  • Organizer: 第11回日本蛋白質科学会年会ワークショップ「タンパク質修飾のイメージング」
  • Place of Presentation: 吹田
  • Year and Date: 20110507-09
  • Invited
• [Presentation] Small molecule screening for epigenetic modulators (2011)
  • Author(s): Hiroshi Kimura.
  • Organizer: JSPS UK/Japan Collaborative Symposium"Interdisciplinary approaches for the study of senescence"
  • Place of Presentation: Cambridge, UK
  • Year and Date: 20110209-10
  • Invited
• [Presentation] Visualizing histone modification dynamics in living cells (2011)
  • Author(s): Hiroshi Kimura
  • Organizer: International Symposium on the Physicochemical Field for Genetic Activities
  • Place of Presentation: Awaji, Japan
  • Year and Date: 20110124-26
  • Invited
• [Presentation] エピジェネティック制御に関わるヒストン修飾の生細胞イメージング (2010)
  • Author(s): 木村宏
  • Organizer: 日本遺伝学会第82回大会シンポジウム「多様な生命現象におけるエピゲノム制御」
  • Place of Presentation: 札幌
  • Year and Date: 20100920-23
  • Invited
• [Presentation] Live cell imaging of epigenetic histone modifications (2010)
  • Author(s): Hiroshi Kimura
  • Organizer: BMB2010・シンポジウム
  • Place of Presentation: 神戸
  • Year and Date: 20100000
  • Invited
• [Presentation] Visualization of epigenetic histone modifications in living cells (2010)
  • Author(s): Hiroshi Kimura
  • Organizer: JSPS Sweden-Japan Joint Colloquium"Epigenetics -new horizons in Japan and Scandinavia-"
  • Place of Presentation: Stockholm, Sweden
  • Year and Date: 2010-09-06
  • Invited
• [Book] 特異的モノクローナル抗体を用いたメチル化ヒストンダイナミクスの可視化,エピジェネティクスと疾患(牛島俊和,塩田邦郎,田嶋正二,吉田稔/編)(実験医学増刊) (2010)
  • Author(s): 木村宏,林陽子
  • Total Pages: 115-121
  • Publisher: 羊土社
• [Remarks]
  • URL: http://www.fbs.osaka-u.ac.jp/labs/hiraoka/kimura/index.html
• [Remarks]
  • URL: http://www.dma.jim.osaka-u.ac.jp/view?l=ja&u=7721