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Research

Research

BDR researchers coming from diverse research fields are working together to achieve higher goals.

Seminars & Symposia

Seminars & Symposia

BDR hosts annual symposium and regular seminars inviting international scientists in life science.

Careers & Study

Careers & Study

BDR embraces people from diverse backgrounds, and strives to create an open and supportive setting for research.

Outreach

Outreach

BDR communicates the appeal and significance of our research to society through the use of various media and activities.

News

News

From research, events, people and everything in between, find out what’s going on at RIKEN BDR.

About Us

About Us

Exploring the scientific foundations of life through interdisciplinary approaches to address society’s problems.

Photo of histon model

Team Leader
Takashi Umehara Ph.D.

Laboratory for Epigenetics Drug Discovery

LocationYokohama / West Bldg. W221

E-mailtakashi.umehara[at]riken.jp

Please replace [at] with @.

Change “added” life info as you like

Epigenetics is a research field that tackles life information that is "added" to genetic information. The major entity of this "addition" is a chemical modification to a complex of a genomic DNA and histone proteins called chromatin. Since epigenetics is involved in the control of cancer, iPS cells and lifespan, it attracts attention as a molecular target for drug discovery, regenerative medicine, and anti-aging. Our laboratory aims to manipulate diseases, iPS cells and anti-aging as desired by developing technologies to precisely reconstitute, detect and control human epigenetic information.

Reconstitution of epigenetics
Synthetic technologies of a protein acetylated as designed. With this technology, transcriptionally active chromatin can be precisely reproduced in vitro.

Detection of epigenetics
Development of an antibody that detects acetylation at two residues in histone H4 tail. With this antibody, transcriptionally hyperactive chromatin can be detected at single nucleosome resolution.

Regulation of epigenetics
Histone demethylase inhibitor S2101 developed based on protein structure. This compound is commercially available as an epigenetics-regulating reagent.

Selected Publications

Niwa H, Watanabe C, Sato S, et al.
Structure–activity relationship and in silico evaluation of cis- and trans-PCPA-derived inhibitors of LSD1 and LSD2.
ACS Medicinal Chemistry Letters 13, 1485-1492 (2022) doi: 10.1021/acsmedchemlett.2c00294

Kikuchi M, Morita S, Goto M, et al.
Elucidation of binding preferences of YEATS domains to site-specific acetylated nucleosome core particles.
Journal of Biological Chemistry 298, 102164 (2022) doi: 10.1016/j.jbc.2022.102164

Sasaki K, Suzuki M, Sonoda T, et al.
Visualization of the dynamic interaction between nucleosomal histone H3K9 tri-methylation and HP1α chromodomain in living cells.
Cell Chemical Biology 29, 1153-1161 (2022) doi: 10.1016/j.chembiol.2022.05.006

Koda Y, Sato S, Yamamoto H, et al.
Design and synthesis of tranylcypromine-derived LSD1 inhibitors with improved hERG and microsomal stability profiles.
ACS Medicinal Chemistry Letters 13, 848-854 (2022) doi: 10.1021/acsmedchemlett.2c00120

Kitagawa H, Kikuchi M, Sato S, et al.
Structure-based identification of potent lysine-specific demethylase 1 inhibitor peptides and temporary cyclization to enhance proteolytic stability and cell growth-inhibitory activity.
Journal of Medicinal Chemistry 64, 3707-3719 (2021) doi: 10.1021/acs.jmedchem.0c01371

Wakamori M, Okabe K, Ura K, et al.
Quantification of the effect of site-specific histone acetylation on chromatin transcription rate.
Nucleic Acids Research 48(22), 12648-12659 (2020) doi: 10.1093/nar/gkaa1050

Wu HD, Kikuchi M, Dagliyan O, et al.
Rational design and implementation of a chemically inducible hetero-trimerization system.
Nature Methods 17, 928-936 (2020) doi: 10.1038/s41592-020-0913-x

Furukawa A, Wakamori M, Arimura Y, et al.
Acetylated histone H4 tail enhances histone H3 tail acetylation by altering their mutual dynamics in the nucleosome.
Proceedings of the National Academy of Sciences USA 117, 19661-19663 (2020) doi: 10.1073/pnas.2010506117

Saito S, Kikuchi J, Koyama D, et al.
Eradication of central nervous system leukemia of T-cell origin with a brain-permeable LSD1 inhibitor.
Clinical Cancer Research 25, 1601-1611 (2019) doi: 10.1158/1078-0432.CCR-18-0919

Handoko L, Kaczkowski B, Hon CC, et al.
JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states.
Epigenetics 13, 410-431 (2018) doi: 10.1080/15592294.2018.1469891

Members

Photo of Team Leader, Takashi Umehara

Team LeaderTakashi Umehara

Senior Technical Scientist*Hideaki Niwa

  • hideaki.niwa[at]riken.jp

Research ScientistMasaki Kikuchi

  • masaki.kikuchi[at]riken.jp

Research ScientistNando Dulal Das

  • nando.das[at]riken.jp

Technical ScientistSatoshi Morita

  • satoshi.morita[at]riken.jp

Technical ScientistMasatoshi Wakamori

  • masatoshi.wakamori[at]riken.jp

Technical ScientistShin Sato

  • shin.sato[at]riken.jp

Technical ScientistHisami Watanabe

  • hisami.watanabe[at]riken.jp

Research FellowDaisuke Aoki

  • daisuke.aoki[at]riken.jp

AssistantYuki Saito

  • yuki.saito[at]riken.jp

(Please replace [at] with @)

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