Basic Information

Faculty

• 医学部

Academic Degree

• 修士（理学）(東京大学)
• 博士（理学）(東京大学)

ID,URL

• J-Global ID

  201801020353159959

researchmap URL

• https://researchmap.jp/7000025208

Research

Research Topics, Overview of the research

• Research Topics

  Understanding molecular mechanisms in DNA double-strand break repair

• Overview of the research

  Radiation and other naturally occurring exogenous and endogenous DNA damage often generate genomic DNA breaks with chemically modified “dirty” ends, and are highly carcinogenic. DNA repair must start by cleaning “dirty” ends (modifying them into a 3′-OH dNMP and a 5′-P dNMP), but much remains unknown about its molecular mechanism. Yamada wants to understand this process and tries to develop a high-resolution bioassay system to monitor how cells make such “dirty” ends “clean” ends.

Research Interests

• human cell culture
• mouse
• fission yeast
• breast cancer
• estrogen
• DNA topoisomerase
• DNA repair
• DNA double strand break
• repetitive DNA
• homologous recombination
• 減数分裂

Research Areas

• Life sciences, Metabolism and endocrinology
• Life sciences, Cell biology
• Life sciences, Laboratory animal science
• Life sciences, Tumor biology
• Life sciences, Molecular biology
• Life sciences, Genetics
• Life sciences, Genomics
• Life sciences, Radiology

Papers

• A central coupler for recombination initiation linking chromosome architecture to S-phase checkpoint

  Ito Masaru; Miyoshi Tomoichiro; Kugou Kazuto; Yamada Shintaro; Furuichi Masaki; Oda Arisa; Yamada Takatomi; Hirota Kouji; Masai Hisao; Ohta Kunihiro

  GENES & GENETIC SYSTEMS, Dec. 2012, Peer-reviewed

  
• ATM suppresses c-Myc overexpression in the mammary epithelium in response to estrogen

  Rifat Ara Najnin; Md Rasel Al Mahmud; Md Maminur Rahman; Shunichi Takeda; Hiroyuki Sasanuma; Hisashi Tanaka; Yasuhiro Murakawa; Naoto Shimizu; Salma Akter; Masatoshi Takagi; Takuro Sunada; Shusuke Akamatsu; Gang He; Junji Itou; Masakazu Toi; Mary Miyaji; Kimiko M. Tsutsui; Scott Keeney; Shintaro Yamada

  Cell Reports, Jan. 2023

  
• Physiological concentrations of glucocorticoids induce pathological DNA double‐strand breaks

  Salma Akter; Akihiro Shimba; Koichi Ikuta; Rasel Al Mahmud; Shintaro Yamada; Hiroyuki Sasanuma; Masataka Tsuda; Masakatsu Sone; Yukio Ago; Kenichi Murai; Hisashi Tanaka; Shunichi Takeda

  Genes to Cells, 22 Nov. 2022, Peer-reviewed

  
• Triple-helix potential of the mouse genome.

  Kaku Maekawa; Shintaro Yamada; Rahul Sharma; Jayanta Chaudhuri; Scott Keeney

  Proceedings of the National Academy of Sciences of the United States of America, 10 May 2022, Peer-reviewed

  
• Restoration of ligatable "clean" double-strand break ends is the rate-limiting step in the rejoining of ionizing-radiation-induced DNA breakage.

  Hiroyuki Sasanuma; Shintaro Yamada; Masataka Tsuda; Shunichi Takeda

  DNA repair, Sep. 2020

  
• Maintenance of meiotic crossover against reduced double-strand break formation in fission yeast lacking histone H2A.Z.

  Takatomi Yamada; Shintaro Yamada; Da-Qiao Ding; Yurika Fujita; Emi Takaya; Yasushi Hiraoka; Hiroshi Murakami; Kunihiro Ohta

  Gene, 15 Jun. 2020, Peer-reviewed

  
• Molecular structures and mechanisms of DNA break processing in mouse meiosis.

  Shintaro Yamada; Anjali Gupta Hinch; Hisashi Kamido; Yongwei Zhang; Winfried Edelmann; Scott Keeney

  Genes & development, 01 Jun. 2020, Peer-reviewed

  
• UBC13-Mediated Ubiquitin Signaling Promotes Removal of Blocking Adducts from DNA Double-Strand Breaks.

  Remi Akagawa; Hai Thanh Trinh; Liton Kumar Saha; Masataka Tsuda; Kouji Hirota; Shintaro Yamada; Atsushi Shibata; Masato T Kanemaki; Shinichiro Nakada; Shunichi Takeda; Hiroyuki Sasanuma

  iScience, 31 Mar. 2020, Peer-reviewed

  
• ATM and PRDM9 regulate SPO11-bound recombination intermediates during meiosis.

  Jacob Paiano; Wei Wu; Shintaro Yamada; Nicholas Sciascia; Elsa Callen; Ana Paola Cotrim; Rajashree A Deshpande; Yaakov Maman; Amanda Day; Tanya T Paull; André Nussenzweig

  Nature communications, 12 Feb. 2020, Peer-reviewed

  
• BRCA1 ensures genome integrity by eliminating estrogen-induced pathological topoisomerase II-DNA complexes.

  Hiroyuki Sasanuma; Masataka Tsuda; Suguru Morimoto; Liton Kumar Saha; Md Maminur Rahman; Yusuke Kiyooka; Haruna Fujiike; Andrew D Cherniack; Junji Itou; Elsa Callen Moreu; Masakazu Toi; Shinichiro Nakada; Hisashi Tanaka; Ken Tsutsui; Shintaro Yamada; Andre Nussenzweig; Shunichi Takeda

  Proceedings of the National Academy of Sciences of the United States of America, 06 Nov. 2018, Peer-reviewed

  
• The conserved histone variant H2A.Z illuminates meiotic recombination initiation.

  Shintaro Yamada; Kazuto Kugou; Da-Qiao Ding; Yurika Fujita; Yasushi Hiraoka; Hiroshi Murakami; Kunihiro Ohta; Takatomi Yamada

  Current genetics, Oct. 2018, Peer-reviewed

  
• The histone variant H2A.Z promotes initiation of meiotic recombination in fission yeast.

  Shintaro Yamada; Kazuto Kugou; Da-Qiao Ding; Yurika Fujita; Yasushi Hiraoka; Hiroshi Murakami; Kunihiro Ohta; Takatomi Yamada

  Nucleic acids research, 25 Jan. 2018, Peer-reviewed

  
• Genomic and chromatin features shaping meiotic double-strand break formation and repair in mice.

  Shintaro Yamada; Seoyoung Kim; Sam E Tischfield; Maria Jasin; Julian Lange; Scott Keeney

  Cell cycle (Georgetown, Tex.), 18 Oct. 2017, Peer-reviewed

  
• Correlation of Meiotic DSB Formation and Transcription Initiation Around Fission Yeast Recombination Hotspots.

  Shintaro Yamada; Mika Okamura; Arisa Oda; Hiroshi Murakami; Kunihiro Ohta; Takatomi Yamada

  Genetics, Jun. 2017, Peer-reviewed

  
• A global view of meiotic double-strand break end resection.

  Eleni P Mimitou; Shintaro Yamada; Scott Keeney

  Science (New York, N.Y.), 06 Jan. 2017, Peer-reviewed

  
• The Landscape of Mouse Meiotic Double-Strand Break Formation, Processing, and Repair.

  Julian Lange; Shintaro Yamada; Sam E Tischfield; Jing Pan; Seoyoung Kim; Xuan Zhu; Nicholas D Socci; Maria Jasin; Scott Keeney

  Cell, 20 Oct. 2016, Peer-reviewed

  
• Acetylated Histone H3K9 is associated with meiotic recombination hotspots, and plays a role in recombination redundantly with other factors including the H3K4 methylase Set1 in fission yeast.

  Shintaro Yamada; Kunihiro Ohta; Takatomi Yamada

  Nucleic acids research, 01 Apr. 2013, Peer-reviewed

  
• A central coupler for recombination initiation linking chromosome architecture to S phase checkpoint.

  Tomoichiro Miyoshi; Masaru Ito; Kazuto Kugou; Shintaro Yamada; Masaki Furuichi; Arisa Oda; Takatomi Yamada; Kouji Hirota; Hisao Masai; Kunihiro Ohta

  Molecular cell, 14 Sep. 2012, Peer-reviewed

  
• Fission yeast ATF/CREB family protein Atf21 plays important roles in production of normal spores.

  Tomohiko Morita; Takatomi Yamada; Shintaro Yamada; Kouji Matsumoto; Kunihiro Ohta

  Genes to cells : devoted to molecular & cellular mechanisms, Feb. 2011, Peer-reviewed

  
• Rec8 guides canonical Spo11 distribution along yeast meiotic chromosomes.

  Kazuto Kugou; Tomoyuki Fukuda; Shintaro Yamada; Masaru Ito; Hiroyuki Sasanuma; Saori Mori; Yuki Katou; Takehiko Itoh; Kouji Matsumoto; Takehiko Shibata; Katsuhiko Shirahige; Kunihiro Ohta

  Molecular biology of the cell, Jul. 2009, Peer-reviewed

  
• XRCC1 counteracts poly(ADP ribose)polymerase (PARP) poisons, olaparib and talazoparib, and a clinical alkylating agent, temozolomide, by promoting the removal of trapped PARP1 from broken DNA.

  Kouji Hirota; Masato Ooka; Naoto Shimizu; Kousei Yamada; Masataka Tsuda; Mahmoud Abdelghany Ibrahim; Shintaro Yamada; Hiroyuki Sasanuma; Mitsuko Masutani; Shunichi Takeda

  Genes to cells : devoted to molecular & cellular mechanisms, 23 Feb. 2022, Peer-reviewed

  

Misc.

• lab report, international studies

  山田真太郎

  Experimental Medicine, Jan. 2019, Invited, Lead author

  
• DNA damage and cancer (Part 2/2)

  山田真太郎

  NY Japion, Sep. 2017, Invited, Lead author

  
• DNA damage and cancer (Part 1/2)

  山田真太郎

  NY Japion, Sep. 2017, Invited, Lead author

  
• Bottlenecks and perspective of studies on non-coding DNA segments

  太田邦史; 久郷和人; 山田真太郎; 小田有沙

  Experimental Medicine, Sep. 2012, Invited

  
• Relationship between meiotic cohesin component Rec8 and DSB proteins

  Kazuto Kugou; Masaru Ito; Tomoyuki Fukuda; Shintaro Yamada; Takehiko Shibata; Katsuhiko Shirahige; Kunihiro Ohta

  GENES & GENETIC SYSTEMS, Dec. 2010

  

Presentations

• ゲノムが潜在的に取り得る三重らせん構造の特徴の理解

  山田真太郎

  東京都医学総合研究所, 12 Jul. 2023, Invited

  
• A functional link between DNA double-strand break repair and the early transcriptional response to the sex hormone

  Shintaro Yamada

  Social DNAing, 29 Jun. 2023, Invited

  
• A functional link between DNA double-strand break repair and the early transcriptional response to the sex hormone.

  Shintaro Yamada

  国立遺伝学研究所, 22 Dec. 2022, Invited

  
• DNA損傷修復応答の破綻による臓器特異的発がん機構

  山田真太郎

  第45回日本分子生物学会年会 日本生物物理学会 共催, 30 Nov. 2022, Invited

  
• Genome-wide identification of androgen-responsive enhancers and analysis of TOP2 function in enhancers

  Shintaro Yamada

  TOPO 2021, 28 May 2021, Invited

  
• DNA Break and Repair in Meiosis

  Shintaro Yamada; Eleni P. Mimitou; Julian Lange; Maria Jasin; Scott Keeney

  第43回日本分子生物学会年会, 04 Dec. 2020, Invited

  
• Mouse meiotic double-strand breaks are underrepresented but nonetheless occur frequently within repeated sequences

  Shintaro Yamada

  The 2017 NYU Repetitive DNA Symposium, 27 Oct. 2017, Invited

  

Awards

• 31 Aug. 2017

  the 2017 FASEB Genetic Recombination and Genome Rearrangements conference, Travel Award
• 22 Mar. 2022

  AMED and New York Academy of Sciences, Interstellar Initiative Alumni Program Outstanding Team Presentation
• 31 Mar. 2008

  The University of Tokyo Faculty of Science, The University of Tokyo Faculty of Science, Elite Science Student Visit Abroad Program
• 31 Mar. 2007

  The University of Tokyo Faculty of Science, The University of Tokyo Faculty of Science, Undergraduate Program for Bioinformatics and Systems Biology
• 01 Apr. 2010

  the Japan Society for the Promotion of Science, Research Fellowship for Young Scientists from the Japan Society for the Promotion of Science
• 09 May 2015

  Japanese Medical Society of America, Kuro Murase MD-JMSA Scholarship
• 16 Nov. 2016

  The 10th 3R Symposium, The 10th 3R Symposium Best Poster Award

External funds: Kakenhi

• Identification of genomic elements that promote hormone-responsive transient expression of oncogenes

  Grant-in-Aid for Scientific Research (C)

  Basic Section 50010:Tumor biology-related

  Kyoto University

  山田 真太郎

  From 01 Apr. 2021, To 31 Mar. 2024, Granted

  性ホルモン;DNAトポイソメラーゼ;DNA二重鎖切断;DNA修復;乳癌

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-21K07148/
• 発癌関連転写制御領域（エンハンサー）の網羅的同定の為の国際共同研究

  Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))

  Medium-sized Section 50:Oncology and related fields

  Institute of Physical and Chemical Research

  村川 泰裕

  From 27 Oct. 2020, To 31 Mar. 2023, Granted

  エンハンサー;遺伝子発現;発がん;ヒトゲノム科学;乳がん;遺伝子発現制御;発癌

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20KK0186/
• Understanding mechanisms in removal of aberrant adducts from ends of genomic DNA breaks caused by radiation and other factors

  Grant-in-Aid for Early-Career Scientists

  Basic Section 63020:Radiation influence-related

  Kyoto University

  Shintaro Yamada

  From 01 Apr. 2019, To 31 Mar. 2021, Project Closed

  DNA二重鎖切断修復;II型DNAトポイソメラーゼ

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-19K20449/
• ゲノム修復の破綻によりホルモン刺激依存的に癌遺伝子が過剰発現するメカニズムの解明

  Fund for the Promotion of Joint International Research (Fostering Joint International Research (A))

  Basic Section 50010:Tumor biology-related

  Kyoto University

  山田 真太郎

  From 01 Apr. 2022, To 31 Mar. 2023, Adopted

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22KK0252/