Modality of nucleosome dynamics

• Project Area: Genome modality: understanding physical properties of the genome
• Project/Area Number: 20H05936
• Research Category: Grant-in-Aid for Transformative Research Areas (A)
• Allocation Type: Single-year Grants
• Review Section: Transformative Research Areas, Section (III)
• Research Institution: National Institute of Genetics
• Principal Investigator: 前島 一博 国立遺伝学研究所, 遺伝メカニズム研究系, 教授 (00392118)
• Co-Investigator(Kenkyū-buntansha): 日比野 佳代 国立遺伝学研究所, 遺伝メカニズム研究系, 助教 (40435673) ; 杉山 弘 京都大学, 高等研究院, 研究員 (50183843) ; 谷口 雄一 京都大学, 高等研究院, 教授 (90556276)
• Project Period (FY): 2020-11-19 – 2025-03-31
• Project Status: Granted (Fiscal Year 2024)
• Budget Amount: ¥182,390,000 (Direct Cost: ¥140,300,000、Indirect Cost: ¥42,090,000); Fiscal Year 2024: ¥35,490,000 (Direct Cost: ¥27,300,000、Indirect Cost: ¥8,190,000); Fiscal Year 2023: ¥35,490,000 (Direct Cost: ¥27,300,000、Indirect Cost: ¥8,190,000); Fiscal Year 2022: ¥35,490,000 (Direct Cost: ¥27,300,000、Indirect Cost: ¥8,190,000); Fiscal Year 2021: ¥33,670,000 (Direct Cost: ¥25,900,000、Indirect Cost: ¥7,770,000); Fiscal Year 2020: ¥42,250,000 (Direct Cost: ¥32,500,000、Indirect Cost: ¥9,750,000)
• Keywords: ヌクレオソーム / クロマチン / 超解像顕微鏡 / ゲノミックス解析 / 原子間力顕微鏡 / ゲノミクス解析 / 超解像イメージング / AFM / PIポリアミド

Outline of Research at the Start

ゲノムクロマチンは一体どのように細胞内に収納され、どのように振る舞うのだろうか?この10年間、代表者らは、細胞のクロマチンは従来考えられてきたような、規則正しく折り畳まれた階層構造ではなく、液体のように不規則でダイナミックな構造であることを明らかにしてきた。本計画研究では、1分子蛍光イメージング(前島・日比野)、ゲノムHi-CO解析(谷口)、高速AFM・DNA配列結合ポリアミドPIP(杉山)を用いて、ゲノムの構造単位であるヌクレオソームレベルでのクロマチン構造と動態の観点から、ゲノムモダリティを理解することを目的とする。

Outline of Annual Research Achievements

本計画研究では、1分子蛍光イメージング(前島・日比野)、ゲノムHi-CO解析(谷口)、高速AFM・DNA配列結合ポリアミドPIP(杉山)を用いて、ゲ ノムの構造単位であるヌクレオソームレベルでのクロマチン構造と動態の観点から、ゲノムモダリティを理解することを目的とする。領域内研 究を通して、関連タンパク質の機能阻害や疾患変異が、間期クロマチンと分裂期染色体organization(組織化)や動態に与える影響を調べ、細胞 機能制御機構やこれらの破綻による疾患の発症機構の理解、さらにはゲノムモダリティ・スィート構築に貢献する。

代表者前島、分担 者日比野らは、1分子・超解像顕微鏡法とタンパク質迅速除去法を組み合わせ、コンデンシンやコヒーシンなどを個別除去した状態で、ヌクレ オソーム動態を1分子計測をおこなった。これにより、これらの因子が染色体凝縮やクロマチン組織化にどのように寄与するかを解析した。 分担者杉山らは、DNA塩基配列特異的結合分子であるピロールーイミダゾールポリアミドを用いて、遺伝子発現をオンーオフする遺伝子スイッチを作成した。オンスイッチとしてミトコンドリアの活性化を行った。さらにミトコンドリアDNAの変異の回復も検討した。またDNAオリガミ法を用いてDNAフレームを作り、葉緑体のタンパクであるHBD1の結合を観察した。分担者谷口らは、Hi-CO法が解析できる対象を、従来の出芽酵母ゲノムからヒトゲノムを含む他のゲノムに拡張するための開発を行った。特に、連結連結反応を行う前に行うゲノムの化学架橋の条件の検討を行った。これまでは一般的な化学架橋剤である、DNA-DNAやDNA-タンパク質間を結合させるホルムアルデヒドを使用してきたが、タンパク質-タンパク質間を結合させる化学架橋剤など、複数の架橋剤について検討を行い、ヌクレオソーム間の結合効率を最適化した。

Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

コンデンシン、コヒーシンの細胞内でのクロマチンに対する役割の一端が明らかになり、計画通りに概ね進んだため。

Strategy for Future Research Activity

計画通りに概ね進んでいるため、さらにクロマチンドメインの物理的描像に迫る。

Research Products

• [Int'l Joint Research] ケント州立大学(米国)
• [Journal Article] Dissection of nanoconfinement and proximity effects on the binding events in DNA origami nanocavity (2022)
  • Author(s): Jonchhe Sagun、Pandey Shankar、Beneze Christian、Emura Tomoko、Sugiyama Hiroshi、Endo Masayuki、Mao Hanbin
  • Journal Title: Nucleic Acids Research Volume: 50 Issue: 2 Pages: 697-703
  • DOI: 10.1093/nar/gkab1298
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Targeted epigenetic induction of mitochondrial biogenesis enhances antitumor immunity in mouse model (2022)
  • Author(s): Malinee Madhu、Pandian Ganesh Namasivayam、Sugiyama Hiroshi
  • Journal Title: Cell Chemical Biology Volume: 29 Issue: 3 Pages: 463-475.e6
  • DOI: 10.1016/j.chembiol.2021.08.001
  • Peer Reviewed / Open Access
• [Journal Article] Targeted elimination of mutated mitochondrial DNA by a multi-functional conjugate capable of sequence-specific adenine alkylation (2022)
  • Author(s): Hidaka Takuya、Hashiya Kaori、Bando Toshikazu、Pandian Ganesh N.、Sugiyama Hiroshi
  • Journal Title: Cell Chemical Biology Volume: 29 Issue: 4 Pages: 1-6
  • DOI: 10.1016/j.chembiol.2021.08.003
  • Peer Reviewed / Open Access
• [Journal Article] The solid and liquid states of chromatin (2021)
  • Author(s): Hansen Jeffrey C.、Maeshima Kazuhiro、Hendzel Michael J.
  • Journal Title: Epigenetics & Chromatin Volume: 14 Issue: 1 Pages: 50-50
  • DOI: 10.1186/s13072-021-00424-5
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Telomere-specific chromatin capture using a pyrrole-imidazole polyamide probe for the identification of proteins and non-coding RNAs (2021)
  • Author(s): Ide Satoru、Sasaki Asuka、Kawamoto Yusuke、Bando Toshikazu、Sugiyama Hiroshi、Maeshima Kazuhiro
  • Journal Title: Epigenetics & Chromatin Volume: 14 Issue: 1 Pages: 46-46
  • DOI: 10.1186/s13072-021-00421-8
  • Peer Reviewed / Open Access
• [Journal Article] The loopy world of cohesin (2021)
  • Author(s): Maeshima Kazuhiro、Iida Shiori
  • Journal Title: eLife Volume: 10
  • DOI: 10.7554/elife.71585
  • Peer Reviewed / Open Access
• [Journal Article] Liquid-like chromatin in the cell: What can we learn from imaging and computational modeling? (2021)
  • Author(s): Itoh Yuji, Woods Esmae J., Minami Katsuhiko, Maeshima Kazuhiro, Collepardo-Guevara Rosana
  • Journal Title: Current Opinion in Structural Biology Volume: 71 Pages: 123-135
  • DOI: 10.1016/j.sbi.2021.06.004
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 3D genomics across the tree of life reveals condensin II as a determinant of architecture type (2021)
  • Author(s): Hoencamp C. et al.
  • Journal Title: Science Volume: 372 Issue: 6545 Pages: 984-989
  • DOI: 10.1126/science.abe2218
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Is transcriptional regulation just going through a phase? (2021)
  • Author(s): Narlikar Geeta J.、Myong Sua、Larson Daniel、Maeshima Kazuhiro、Francis Nicole、Rippe Karsten、Sabari Benjamin、Strader Lucia、Tjian Robert
  • Journal Title: Molecular Cell Volume: 81 Issue: 8 Pages: 1579-1585
  • DOI: 10.1016/j.molcel.2021.03.046
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Physical nature of chromatin in the nucleus. (2021)
  • Author(s): Maeshima, K., Iida, S., Tamura, S.
  • Journal Title: Cold Spring Harbor Perspectives in Biology Volume: 13
  • Peer Reviewed / Open Access
• [Journal Article] Hexanediol Condenses Chromatin (2021)
  • Author(s): ITOH Yuji、IDE Satoru、MAESHIMA Kazuhiro
  • Journal Title: Seibutsu Butsuri Volume: 61 Issue: 6 Pages: 385-388
  • DOI: 10.2142/biophys.61.385
  • NAID: 130008120205
  • ISSN: 0582-4052, 1347-4219
  • Peer Reviewed / Open Access
• [Journal Article] Application of DNA‐Alkylating Pyrrole‐Imidazole Polyamides for Cancer Treatment (2021)
  • Author(s): Maeda Rina、Bando Toshikazu、Sugiyama Hiroshi
  • Journal Title: ChemBioChem Volume: 22 Issue: 9 Pages: 1538-1545
  • DOI: 10.1002/cbic.202000752
  • Peer Reviewed / Open Access
• [Journal Article] HBD1 protein with a tandem repeat of two HMG-box domains is a DNA clip to organize chloroplast nucleoids in <i>Chlamydomonas reinhardtii</i> (2021)
  • Author(s): Takusagawa Mari、Kobayashi Yusuke、Fukao Yoichiro、Hidaka Kumi、Endo Masayuki、Sugiyama Hiroshi、Hamaji Takashi、Kato Yoshinobu、Miyakawa Isamu、Misumi Osami、Shikanai Toshiharu、Nishimura Yoshiki
  • Journal Title: Proceedings of the National Academy of Sciences Volume: 118 Issue: 20 Pages: 463-475
  • DOI: 10.1073/pnas.2021053118
  • NAID: 120007035840
  • Peer Reviewed / Open Access
• [Journal Article] Non‐invasive Regulation of Cellular Morphology Using a Photoswitchable Mechanical DNA Polymer (2021)
  • Author(s): Sethi Soumya、Hidaka Kumi、Sugiyama Hiroshi、Endo Masayuki
  • Journal Title: Angewandte Chemie International Edition Volume: 60 Issue: 37 Pages: 20342-20349
  • DOI: 10.1002/anie.202105425
  • Peer Reviewed
• [Journal Article] Photo-Controllable Phase Transition of Arylazopyrazole-Conjugated Oligonucleotides (2021)
  • Author(s): Hidaka Takuya、Wee Wen Ann、Yum Ji Hye、Sugiyama Hiroshi、Park Soyoung
  • Journal Title: Bioconjugate Chemistry Volume: 32 Issue: 10 Pages: 2129-2133
  • DOI: 10.1021/acs.bioconjchem.1c00302
  • Peer Reviewed / Open Access
• [Journal Article] Strong and Specific Recognition of CAG/CTG Repeat DNA (5’‐dWGCWGCW‐3’) by a Cyclic Pyrrole‐Imidazole Polyamide (2021)
  • Author(s): Hirose Yuki、Ohno Tomo、Asamitsu Sefan、Hashiya Kaori、Bando Toshikazu、Sugiyama Hiroshi
  • Journal Title: ChemBioChem Volume: 23 Issue: 2
  • DOI: 10.1002/cbic.202100533
  • Peer Reviewed / Open Access
• [Journal Article] Hi-CO: 3D genome structure analysis with nucleosome resolution (2021)
  • Author(s): Ohno Masae、Ando Tadashi、Priest David G.、Taniguchi Yuichi
  • Journal Title: Nature Protocols Volume: 16 Issue: 7 Pages: 3439-3469
  • DOI: 10.1038/s41596-021-00543-z
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] iNucs: inter-nucleosome interactions (2021)
  • Author(s): Oveisi Mehrdad、Shukla Manu、Seymen Nogayhan、Ohno Masae、Taniguchi Yuichi、Nahata Sunil、Loos Remco、Mufti Ghulam J、Allshire Robin C、Dimitrov Stefan、Karimi Mohammad M
  • Journal Title: Bioinformatics Volume: 37 Issue: 23 Pages: 4562-4563
  • DOI: 10.1093/bioinformatics/btab698
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 1,6-hexanediol rapidly immobilizes and condenses chromatin in living human cells (2021)
  • Author(s): Itoh Yuji、Iida Shiori、Tamura Sachiko、Nagashima Ryosuke、Shiraki Kentaro、Goto Tatsuhiko、Hibino Kayo、Ide Satoru、Maeshima Kazuhiro
  • Journal Title: Life Science Alliance Volume: 4 Issue: 4 Pages: e202001005-e202001005
  • DOI: 10.26508/lsa.202001005
  • Peer Reviewed / Open Access
• [Journal Article] Direct Observation of Dynamic Interactions between Orientation‐Controlled Nucleosomes in a DNA Origami Frame (2020)
  • Author(s): Feng Yihong、Hashiya Fumitaka、Hidaka Kumi、Sugiyama Hiroshi、Endo Masayuki
  • Journal Title: Chemistry A European Journal Volume: 26 Issue: 66 Pages: 15282-15289
  • DOI: 10.1002/chem.202003071
  • Peer Reviewed
• [Journal Article] A Near-Infrared Fluorogenic Pyrrole Imidazole Polyamide Probe for Live-Cell Imaging of Telomeres (2020)
  • Author(s): Tsubono Yutaro、Kawamoto Yusuke、Hidaka Takuya、Pandian Ganesh N.、Hashiya Kaori、Bando Toshikazu、Sugiyama Hiroshi
  • Journal Title: Journal of the American Chemical Society Volume: 142 Issue: 41 Pages: 17356-17363
  • DOI: 10.1021/jacs.0c04955
  • Peer Reviewed / Int'l Joint Research
• [Presentation] 分子解像度での生命理解に向けて (2022)
  • Author(s): 谷口雄一
  • Organizer: 東大物性研ワークショップ：開放系トポロジーと生体・量子・統計物理
  • Invited
• [Presentation] Nucleosome-level 3D organization of the genome (2022)
  • Author(s): Taniguchi, Y.
  • Organizer: 2nd WPI NanoLSI-iCeMS Joint Symposium
  • Int'l Joint Research / Invited
• [Presentation] Local chromatin motion is steady during interphase cell cycle and independent of nuclear size and genome chromatin density (2021)
  • Author(s): Kazuhiro Maeshima
  • Organizer: 1AW-08 Temporal and spatial dynamics of genome organization and function. 第44回日本分子生物学会年会
  • Int'l Joint Research / Invited
• [Presentation] Local chromatin motion is steady during interphase cell cycle and independent of nuclear size and genome chromatin density (2021)
  • Author(s): Kazuhiro Maeshima
  • Organizer: The 59th Annual Meeting of the Biophysical Society of Japan
  • Int'l Joint Research / Invited
• [Presentation] Single nucleosome imaging sheds light on the dynamic organization of the human chromosomes. (2021)
  • Author(s): Hibino, K.
  • Organizer: The 44th Annual Meeting of The Molecular Biology Society of Japan
  • Int'l Joint Research / Invited
• [Presentation] Single molecule imaging unveils the dynamic organization of the human chromosomes. (2021)
  • Author(s): Hibino, K.
  • Organizer: The 59th Annual Meeting of the Biophysical Society of Japan, Sendai
  • Int'l Joint Research / Invited
• [Presentation] Nucleosome-level 3D organization of the genome (2021)
  • Author(s): Taniguchi, Y.
  • Organizer: Pacifichem
  • Int'l Joint Research / Invited
• [Presentation] 生命の設計図「ゲノム」の形を探る (2021)
  • Author(s): 谷口雄一
  • Organizer: 第39回大阪科学賞表彰式・記念講演
  • Invited
• [Presentation] １分子検出に基づく次世代型生化学分析法の開発 (2021)
  • Author(s): 谷口雄一
  • Organizer: ARO協議会第8回学術集会
  • Invited
• [Presentation] Nucleosome-level 3D organization of the genome (2021)
  • Author(s): Taniguchi, Y.
  • Organizer: CMUH-iCeMS Joint Meeting
  • Int'l Joint Research / Invited
• [Presentation] Nucleosome-level 3D organization of the yeast genome (2021)
  • Author(s): Taniguchi, Y.
  • Organizer: Cold Spring Harbor Asia Conference: Yeast and life science
  • Int'l Joint Research / Invited
• [Presentation] 分子感度の生化学分析技術の開発 (2021)
  • Author(s): 谷口雄一
  • Organizer: AMED難治性疾患実用化研究事業2020年度成果報告会
  • Invited
• [Presentation] １分子感度での生化学分析 (2021)
  • Author(s): 谷口雄一
  • Organizer: 第75回日本口腔科学会学術集会
  • Invited
• [Presentation] Molecular-resolved biology for understanding complex Biosystems (2021)
  • Author(s): Taniguchi, Y.
  • Organizer: iCeMS-MacDiarmid Institute Online Workshop
  • Int'l Joint Research / Invited
• [Presentation] 一分子ヌクレオソームイメージングによって明らかにする 生細胞のクロマチン環境とその外的影響 (2021)
  • Author(s): 前島一博
  • Organizer: 第14回日本エピジェネティクス研究会年会
  • Invited
• [Presentation] Chromatin behavior in living cells revealed by single-nucleosome imaging (2021)
  • Author(s): Kazuhiro Maeshima
  • Organizer: Cambridge University Biological Society
  • Int'l Joint Research / Invited
• [Presentation] 転写装置によるクロマチン動態制御の解明 (2021)
  • Author(s): 前島一博
  • Organizer: 新学術領域研究クロマチン潜在能Farewell Mini-symposium
  • Invited
• [Presentation] Revealing nucleosome-resolved 3D genome architecture. (2021)
  • Author(s): Taniguchi, Y.
  • Organizer: RIKEN BDR Symposium 2021
  • Invited
• [Presentation] ピロールイミダゾールポリアミドを基盤とした人工遺伝子スイッチ (2021)
  • Author(s): 杉山 弘
  • Organizer: 第399回発生研セミナー
  • Invited
• [Presentation] Pyrrole-Imidazole Polyamides as artificial genetic switches (2021)
  • Author(s): Hiroshi Sugiyama
  • Organizer: the Asian Chemical Biology Initiative (ACBI 2021 Online Meeting)
  • Invited
• [Remarks] ヘキサンジオールは細胞内のクロマチンの動きを止める
  • URL: https://www.nig.ac.jp/nig/ja/2021/02/research-highlights_ja/rh20210204.html