Elucidating the process of enhancer island formation during B cell activation

• Project/Area Number: 19H03210
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Review Section: Basic Section 43050:Genome biology-related
• Research Institution: Osaka University
• Principal Investigator: Nimura Keisuke 大阪大学, 大学院医学系研究科, 准教授 (00462713)
• Project Period (FY): 2019-04-01 – 2022-03-31
• Project Status: Completed (Fiscal Year 2022)
• Budget Amount: ¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000); Fiscal Year 2021: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2020: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000); Fiscal Year 2019: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
• Keywords: 転写ユニティー / 遺伝子発現 / DNAバーコード / 多因子間相互作用 / 転写 / 分子間相互作用解析法 / 分子間相互作用 / エンハンサーアイランド / エンハンサー / クロマチン / 静止期 / B細胞

Outline of Research at the Start

脾臓に存在するB細胞はクロマチン構造が極めて凝集した静止期状態で存在するが、抗原を感知すると24時間以内に急速に活性化し、細胞の体積が増大し、転写量が約10倍に亢進する。一方で、急速に必要な遺伝子群を発現させるためには、静止期状態のクロマチン構造が急速な活性化に備えている必要があるが、そのメカニズムは不明である。これまでの研究から静止期B細胞は島状にH3K27アセチル化領域が凝集した「エンハンサーアイランド」を形成することを見出した。本研究では、このエンハンサーアイランドという新概念を導入し、静止期B細胞が急速な活性化に備えて、どのようにクロマチン状態を制御するか、その機構の解明を目指す。

Outline of Final Research Achievements

A vast number of proteins and RNAs regulate gene expression. It is difficult with current technology to quantitatively measure the complex interactions formed among these multifactorial proteins and RNAs. Therefore, we aimed to establish a novel method for analyzing multifactorial interactions using next-generation sequencing to measure these multifactorial interactions quantitatively. PCR reactions ligated between DNA barcodes conjugated to antibodies against multiple factors that regulate transcription in polymers. Analysis of the data showed that this method could detect multifactorial interactions. This data suggests that this method can detect multifactor interactions.

Academic Significance and Societal Importance of the Research Achievements

本研究成果からDNAバーコードを付加した抗体とポリマーを用いて細胞を封入し、PCR反応を行うことで、多因子間の相互作用を次世代シークエンシングによって解析できる方法を開発するための基盤を構築することができた。本法を用いることで、微量なヒト組織検体などにおいてタンパク質間の相互作用が検出できるようになり、新たな組織検体の評価法になり得る。

Research Products

• [Journal Article] Design and synthesis of ether derivatives of spliceostatin A and their biological evaluation towards prostate cancer treatment (2023)
  • Author(s): Hirabayashi Satoru、Li Yue、Ohta Noriko、Ishibashi Airi、Yoshikawa Yusuke、Lin Bangzhong、Fumimoto Megumi、Takehara Tsunayoshi、Nunomura Kazuto、Suzuki Takeyuki、Haruta Junichi、Nimura Keisuke、Arisawa Mitsuhiro
  • Journal Title: Tetrahedron Letters Volume: 114 Pages: 154288-154288
  • DOI: 10.1016/j.tetlet.2022.154288
  • Peer Reviewed / Open Access
• [Journal Article] Pilot study for the treatment of cutaneous neurofibromas in neurofibromatosis type 1 patients using topical sirolimus gel (2023)
  • Author(s): Wataya-Kaneda Mari、Watanabe Yoshiyuki、Nakamura Ayumi、Yamamoto Kouji、Okada Kiyoshi、Maeda Shinichiro、Nimura Keisuke、Saga Kotaro、Katayama Ichiro
  • Journal Title: Journal of the American Academy of Dermatology Volume: 88 Issue: 4 Pages: 877-880
  • DOI: 10.1016/j.jaad.2022.08.066
  • Peer Reviewed
• [Journal Article] Dual function of SF3B2 on chromatin and RNA to regulate transcription in head and neck squamous cell carcinoma (2022)
  • Author(s): Kitamura Koji、Suzuki Hidefumi、Abe Ryota、Inohara Hidenori、Kaneda Yasufumi、Takahashi Hidehisa、Nimura Keisuke
  • Journal Title: Cell & Bioscience Volume: 12 Issue: 1 Pages: 92-92
  • DOI: 10.1186/s13578-022-00812-8
  • Peer Reviewed / Open Access
• [Journal Article] DNA barcoding and gene expression recording reveal the presence of cancer cells with unique properties during tumor progression (2022)
  • Author(s): Umeki Yuka、Ogawa Noriaki、Uegaki Yuko、Saga Kotaro、Kaneda Yasufumi、Nimura Keisuke
  • Journal Title: Cellular and Molecular Life Sciences Volume: 80 Issue: 1 Pages: 17-17
  • DOI: 10.1007/s00018-022-04640-4
  • Peer Reviewed / Open Access
• [Journal Article] Identification of Malignant Cell Populations Associated with Poor Prognosis in High-Grade Serous Ovarian Cancer Using Single-Cell RNA Sequencing (2022)
  • Author(s): Sumitani Naoki、Ishida Kyoso、Sawada Kenjiro、Kimura Tadashi、Kaneda Yasufumi、Nimura Keisuke
  • Journal Title: Cancers Volume: 14 Issue: 15 Pages: 3580-3580
  • DOI: 10.3390/cancers14153580
  • Peer Reviewed / Open Access
• [Journal Article] Peroxisomal membrane protein PMP34 is involved in the human papillomavirus infection pathway. (2022)
  • Author(s): Ito R, Kitamura K, Inohara H, Yusa K, Kaneda Y, Nimura K.
  • Journal Title: Front Virol. Volume: - Pages: 870922-870922
  • DOI: 10.3389/fviro.2022.870922
  • Peer Reviewed / Open Access
• [Journal Article] Design and Synthesis of 1,2-Deoxy-pyranose Derivatives of Spliceostatin A toward Prostate Cancer Treatment (2020)
  • Author(s): Yoshikawa Yusuke、Ishibashi Airi、Takehara Tsunayoshi、Suzuki Takeyuki、Murai Kenichi、Kaneda Yasufumi、Nimura Keisuke、Arisawa Mitsuhiro
  • Journal Title: ACS Medicinal Chemistry Letters Volume: as soon as Issue: 6 Pages: 1310-1315
  • DOI: 10.1021/acsmedchemlett.0c00153
  • Peer Reviewed / Open Access
• [Journal Article] A simple method using CRISPR-Cas9 to knock-out genes in murine cancerous cell lines (2020)
  • Author(s): Ishibashi Airi、Saga Kotaro、Hisatomi Yuuta、Li Yue、Kaneda Yasufumi、Nimura Keisuke
  • Journal Title: Scientific Reports Volume: 10 Issue: 1 Pages: 22345-22345
  • DOI: 10.1038/s41598-020-79303-0
  • Peer Reviewed / Open Access
• [Journal Article] Evaluation of HPV16 E7 expression in head and neck carcinoma cell lines and clinical specimens (2020)
  • Author(s): Kitamura K, Nimura K(corresponding author), Ito R, Saga K, Inohara H & Kaneda Y
  • Journal Title: Scientific Reports Volume: 10 Issue: 1 Pages: 22138-22138
  • DOI: 10.1038/s41598-020-78345-8
  • Peer Reviewed / Open Access
• [Presentation] 多因子間相互作用による遺伝子発現制御機構の解明 (2022)
  • Author(s): 二村圭祐
  • Organizer: 日本分子生物学会
  • Invited
• [Patent(Industrial Property Rights)] 生体試料中の多因子間相互作用を同定する方法およびキット (2022)
  • Inventor(s): 二村圭祐
  • Industrial Property Rights Holder: 二村圭祐
  • Industrial Property Rights Type: 特許
  • Industrial Property Number: 2022-068519
  • Filing Date: 2022
  • Overseas