組織内の核内ゲノム構造を単一細胞レベルで高解像度に解析する技術の開発

2021 Fiscal Year Annual Research Report

• Project/Area Number: 20K21398
• Research Institution: Kyushu University
• Principal Investigator: 大川 恭行 九州大学, 生体防御医学研究所, 教授 (80448430)
• Project Period (FY): 2020-07-30 – 2022-03-31
• Keywords: エピゲノム / クロマチン / マルチオミクス / 空間オミクス

Outline of Annual Research Achievements

生体は幹細胞あるいは前駆細胞が増殖分化することで、様々な機能を担う細胞、組織が分化増殖することにより形成される。この際に行われるのが選択的な遺伝子発現である。選択的遺伝子発現は、ゲノム領域に広範に分布する遺伝子の制御領域（エンハンサー、プロモーター）を介して特定の遺伝子座を活性化型クロマチン構造に変換し、遺伝子の転写活性を促進するゲノム構造を獲得させるダイナミックなイベントである。一方で、組織形成においては、様々な細胞が、増殖、分化していく極めて不均一な集団変化が起こり、その上個々の細胞においても少なくとも３０００遺伝子座以上が協調的あるいは排他的に秩序だった制御を受け、遺伝子発現あるいは抑制に必要な高次構造の変換が行われる。特定の細胞分化・組織形成を理解するためには、全ゲノム上の遺伝子を対象とし不均一な組織細胞を単一細胞レベルで時系列変化を解析し理解する必要がある。そこで本研究では、新技術LabelingSeq法（仮名称）の開発を行い、予備実験に基づいたパイロット実験を行うことで実証研究を行うことを目的として進めている。各細胞に固有のバーコードを付加する基本技術の構築を行い理論的におおよそ２０００万細胞の固有ラベルを達成する技術を開発し、今年度は、更に、エピゲノム解析への適応を検証した。これら技術は所属機関を通じて知的財産の申請を進めており、現在、エピゲノム・トランスクリプトーム同時解析技術として論文投稿準備中である。

Research Products

• [Journal Article] Uhrf1 governs the proliferation and differentiation of muscle satellite cells. (2022)
  • Author(s): Sakai H, Sawada Y, Tokunaga N, Tanaka K, Nakagawa S, Sakakibara I, Ono Y, Fukada SI, Ohkawa Y, Kikugawa T, Saika T, Imai Y.
  • Journal Title: iScience. Volume: 25 Pages: 103928
  • DOI: 10.1016/j.isci.2022.103928.
  • Peer Reviewed / Open Access
• [Journal Article] Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant. (2022)
  • Author(s): Hirai S, Tomimatsu K, Miyawaki-Kuwakado A, Takizawa Y, Komatsu T, Tachibana T, Fukushima Y, Takeda Y, Negishi L, Kujirai T, Koyama M, Ohkawa Y, Kurumizaka H.
  • Journal Title: Nucleic Acids Res. Volume: 50 Pages: 72-91
  • DOI: 10.1093/nar/gkab1137.
  • Peer Reviewed / Open Access
• [Journal Article] Uterus-specific transcriptional regulation underlies eggshell pigment production in Japanese quail. (2022)
  • Author(s): Ishishita S, Kitahara S, Takahashi M, Iwasaki S, Tatsumoto S, Hara I, Kaneko Y, Kinoshita K, Yamaguchi K, Harada A, Ohmori Y, Ohkawa Y, Go Y, Shigenobu S, Matsuda Y, Suzuki T.
  • Journal Title: PLoS One. Volume: 17 Pages: e0265008
  • DOI: 10.1371/journal.pone.
  • Peer Reviewed / Open Access
• [Journal Article] Direct Conversion of Human Endothelial Cells Into Liver Cancer-Forming Cells Using Nonintegrative Episomal Vectors. (2022)
  • Author(s): Goya T, Horisawa K, Udono M, Ohkawa Y, Ogawa Y, Sekiya S, Suzuki A.
  • Journal Title: Hepatol Commun. Volume: - Pages: -
  • DOI: 10.1002/hep4.1911.
  • Peer Reviewed / Open Access
• [Journal Article] Live imaging of transcription sites using an elongating RNA polymerase II-specific probe. (2022)
  • Author(s): Uchino S, Ito Y, Sato Y, Handa T, Ohkawa Y, Tokunaga M, Kimura H.
  • Journal Title: J Cell Biol. Volume: 221 Pages: e202104134
  • DOI: 10.1083/jcb.202104134.
  • Peer Reviewed / Open Access
• [Journal Article] Relayed signaling between mesenchymal progenitors and muscle stem cells ensures adaptive stem cell response to increased mechanical load. (2021)
  • Author(s): Kaneshige A, Kaji T, Zhang L, Saito H, Nakamura A, Kurosawa T, Ikemoto-Uezumi M, Tsujikawa K, Seno S, Hori M, Saito Y, Matozaki T, Maehara K, Ohkawa Y, Potente M, Watanabe S, Braun T, Uezumi A, Fukada SI.
  • Journal Title: Cell Stem Cell. Volume: 29 Pages: 265-280.e6
  • DOI: 10.1016/j.stem.2021.11.003.
  • Peer Reviewed / Open Access
• [Journal Article] Recent advances in single-cell epigenomics. (2021)
  • Author(s): Harada A, Kimura H, Ohkawa Y.
  • Journal Title: Curr Opin Struct Biol. Volume: 71 Pages: 116-122
  • DOI: 10.1016/j.sbi.
  • Peer Reviewed / Open Access
• [Journal Article] High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq). (2021)
  • Author(s): Bartlett DA, Dileep V, Handa T, Ohkawa Y, Kimura H, Henikoff S, Gilbert DM.
  • Journal Title: J Cell Biol. Volume: 220 Pages: e202103078
  • DOI: 10.1083/jcb.202103078.
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Chromatin loading of MCM hexamers is associated with di-/tri-methylation of histone H4K20 toward S phase entry. (2021)
  • Author(s): Hayashi-Takanaka Y, Hayashi Y, Hirano Y, Miyawaki-Kuwakado A, Ohkawa Y, Obuse C, Kimura H, Haraguchi T, Hiraoka Y.
  • Journal Title: Nucleic Acids Res. Volume: 49 Pages: 12152-12166
  • DOI: 10.1093/nar/gkab1068.
  • Peer Reviewed / Open Access
• [Journal Article] Discriminative feature of cells characterizes cell populations of interest by a small subset of genes. (2021)
  • Author(s): Fujii T, Maehara K, Fujita M, Ohkawa Y.
  • Journal Title: PLoS Comput Biol. Volume: 17 Pages: e1009579
  • DOI: 10.1371/journal.pcbi.1009579.
  • Peer Reviewed / Open Access
• [Journal Article] Sex differences in metabolic pathways are regulated by Pfkfb3 and Pdk4 expression in rodent muscle. (2021)
  • Author(s): Christianto A, Baba T, Takahashi F, Inui K, Inoue M, Suyama M, Ono Y, Ohkawa Y, Morohashi KI.
  • Journal Title: Commun Biol. Volume: 4 Pages: 1264
  • DOI: 10.1038/s42003-021-02790-y.
  • Peer Reviewed / Open Access
• [Journal Article] Neural stem/precursor cells dynamically change their epigenetic landscape to differentially respond to BMP signaling for fate switching during brain development. (2021)
  • Author(s): Katada S, Takouda J, Nakagawa T, Honda M, Igarashi K, Imamura T, Ohkawa Y, Sato S, Kurumizaka H, Nakashima K.
  • Journal Title: Genes Dev. Volume: 35 Pages: 1431-1444
  • DOI: 10.1101/gad.348797.
  • Peer Reviewed / Open Access
• [Journal Article] Modeling population size independent tissue epigenomes by ChIL-seq with single thin sections. (2021)
  • Author(s): Maehara K, Tomimatsu K, Harada A, Tanaka K, Sato S, Fukuoka M, Okada S, Handa T, Kurumizaka H, Saitoh N, Kimura H, Ohkawa Y.
  • Journal Title: Mol Syst Biol. Volume: 17 Pages: e10323
  • DOI: 10.15252/msb.
  • Peer Reviewed / Open Access
• [Journal Article] Genome-wide analysis of chromatin structure changes upon MyoD binding in proliferative myoblasts during the cell cycle. (2021)
  • Author(s): Wu Q, Fujii T, Harada A, Tomimatsu K, Miyawaki-Kuwakado A, Fujita M, Maehara K, Ohkawa Y.
  • Journal Title: J Biochem. Volume: 169 Pages: 653-661
  • DOI: 10.1093/jb/mvab001.
  • Peer Reviewed / Open Access
• [Journal Article] Integrated Analysis of Transcriptome and Histone Modifications in Granulosa Cells During Ovulation in Female Mice. (2021)
  • Author(s): Shirafuta Y, Tamura I, Ohkawa Y, Maekawa R, Doi-Tanaka Y, Takagi H, Mihara Y, Shinagawa M, Taketani T, Sato S, Tamura H, Sugino N.
  • Journal Title: Endocrinology. Volume: 162 Pages: bqab128
  • DOI: 10.1210/endocr/bqab128.
  • Peer Reviewed / Open Access
• [Journal Article] An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver. (2021)
  • Author(s): Matsuzaki F, Uda S, Yamauchi Y, Matsumoto M, Soga T, Maehara K, Ohkawa Y, Nakayama KI, Kuroda S, Kubota H.
  • Journal Title: Cell Rep. Volume: 36 Pages: 109569.
  • DOI: 10.1016/j.celrep.2021.
  • Peer Reviewed / Open Access
• [Journal Article] Targeted inhibition of EPAS1-driven IL-31 production by a small-molecule compound. (2021)
  • Author(s): Kamikaseda Y, Uruno T, Kunimura K, Harada A, Saiki K, Oisaki K, Sakata D, Nakahara T, Kido-Nakahara M, Kanai M, Nakamura S, Ohkawa Y, Furue M, Fukui Y.
  • Journal Title: J Allergy Clin Immunol. Volume: 148 Pages: 633-638
  • DOI: 10.1016/j.jaci.2021.03.029.
  • Peer Reviewed / Open Access
• [Journal Article] High-depth spatial transcriptome analysis by photo-isolation chemistry. (2021)
  • Author(s): Honda M, Oki S, Kimura R, Harada A, Maehara K, Tanaka K, Meno C, Ohkawa Y.
  • Journal Title: Nat Commun. Volume: 12 Pages: 4416
  • DOI: 10.1038/s41467-021-24691-8.
  • Peer Reviewed / Open Access
• [Journal Article] Transcriptome analysis of gene expression changes upon enzymatic dissociation in skeletal myoblasts. (2021)
  • Author(s): Miyawaki-Kuwakado A, Wu Q, Harada A, Tomimatsu K, Fujii T, Maehara K, Ohkawa Y.
  • Journal Title: Genes Cells. Volume: 26 Pages: 530-540
  • DOI: 10.1111/gtc.12870.
  • Peer Reviewed / Open Access
• [Journal Article] Hoxa10 mediates positional memory to govern stem cell function in adult skeletal muscle. (2021)
  • Author(s): Yoshioka K, Nagahisa H, Miura F, Araki H, Kamei Y, Kitajima Y, Seko D, Nogami J, Tsuchiya Y, Okazaki N, Yonekura A, Ohba S, Sumita Y, Chiba K, Ito K, Asahina I, Ogawa Y, Ito T, Ohkawa Y, Ono Y.
  • Journal Title: Sci Adv. Volume: 7 Pages: eabd7924
  • DOI: 10.1126/sciadv.abd7924.20.
  • Peer Reviewed / Open Access
• [Journal Article] Totipotency of mouse zygotes extends to single blastomeres of embryos at the four-cell stage. (2021)
  • Author(s): Maemura M, Taketsuru H, Nakajima Y, Shao R, Kakihara A, Nogami J, Ohkawa Y, Tsukada YI.
  • Journal Title: Sci Rep. Volume: 11 Pages: 11167
  • DOI: 10.1038/s41598-021-90653-1.
  • Peer Reviewed / Open Access
• [Journal Article] Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay. (2021)
  • Author(s): Tachiwana H, Dacher M, Maehara K, Harada A, Seto Y, Katayama R, Ohkawa Y, Kimura H, Kurumizaka H, Saitoh N.
  • Journal Title: Elife Volume: 10 Pages: e66290
  • DOI: 10.7554/eLife.66290.
  • Peer Reviewed / Open Access
• [Presentation] 骨格筋再性能を制御するクロマチン構造等その破綻 (2021)
  • Author(s): 大川恭行
  • Organizer: 第94回日本生化学会大会
  • Invited
• [Presentation] 空間マルチオミクスの展開～エピゲノム, トランスクリプトームからプロテオームの空間計測の試み～ (2021)
  • Author(s): 大川恭行
  • Organizer: がん研セミナー
  • Invited
• [Presentation] Identification and Analysis of Minor Histone Variants (2021)
  • Author(s): Yasuyuki Ohkawa
  • Organizer: EMBO Workshop Physiology and function of histone variants
• [Book] 日本生化学会 (2021)
  • Author(s): 原田 哲仁，大川 恭行
  • Total Pages: -
  • Publisher: Journal of Japanese Biochemical Society
• [Book] 実験医学2021年9月号 (2021)
  • Author(s): 沖 真弥、大川 恭行
  • Total Pages: 131
  • Publisher: 羊土社
  • ISBN: 978-4-7581-2547-5
• [Book] 遺伝子医学MOOK36 (2021)
  • Author(s): 富松航佑, 大川 恭行
  • Total Pages: 218
  • Publisher: 株式会社メディカルドゥ
• [Remarks] 九州大学 トランスクリプトミクス分野ホームページ
  • URL: https://tx.bioreg.kyushu-u.ac.jp/