Chief Scientist Laboratories Cellular Memory Laboratory

Chief Scientist: Yoichi Shinkai (Ph.D.)

Japanese Page

Research Summary

Our laboratory's principal objective is to understand the molecular mechanism of epigenetic gene regulation and the role of epigenetics in health and disease. To address these topics, we take multidisciplinary approaches, including molecular biology, biochemistry, cell biology, structural biology and mouse molecular genetics.

Main Research Fields

Biology

Related Research Fields

Biological Sciences
Molecular biology

Keywords

Epigenetics

Selected Publications

1. Shimazu T*#. Yoshimoto R#. Kotoshiba K. Suzuki T. Matoba S. Hirose M. Akakabe M. Sohtome Y. Sodeoka M. Ogura A. Dohmae N. Shinkai Y*.:
"Histidine N1-position-specific methyltransferase CARNMT1 targets C3H Zinc finger proteins and modulates RNA metabolism"
Genes Dev. 37:724-742. (2023)
2. Fukuda K*. Shimi T. Shimura C. Ono T. Suzuki T. Onoue K. Okayama S. Miura H. Hiratani I. Ikeda K. Okada Y. Dohmae N. Yonemura S. Inoue A. Kimura H. Shinkai Y*.:
"Epigenetic plasticity safeguards heterochromatin configuration in mammals"
Nucleic Acids Res. 51:6190-6207. (2023)
3. Yamada A#. Hirasawa T#. Nishimura K. Shimura C. Kogo N. Fukuda K. Kato M. Yokomori M. Hayashi T. Umeda M. Yoshimura M. Iwakura Y. Nikaido I. Itohara S. Shinkai Y*.
"Derepression of inflammation-related genes link to microglia activation and neural maturation defect in a mouse model of Kleefstra Syndrome"
iScience 24:102741. (2021)
4. Fukuda K*. Shimura C. Miura H. Tanigawa A. Suzuki T. Dohmae D. Hiratani I. Shinkai Y*.
"Regulation of mammalian 3D genome organization and histone H3K9 dimethylation by H3K9 methyltransferases"
Communications Biology 4(1):571. (2021)
5. Davydova E#. Shimazu T#. Schuhmacher M.K. Jakobsson M.E. Willemen H.L.D.M. Liu T. Moen A. Ho A.Y.Y. Ma?ecki J. Schroer L. Pinto R. Suzuki T. Gronsberg I.A. Sohtome Y. Akabane M. Weirich S. Kikuchi M. Olsen J.V. Dohmae N. Umehara T. Sodeoka M. Siino V. McDonough M. Eijkelkamp N. Schofield C.J. Jeltsch A*. Shinkai Y*. Falnes P.O*.
"The methyltransferase METTL9 mediates pervasive 1-methylhistidine modification in mammalian proteomes"
Nat Commun. 2:891. (2021)
6. Tsusaka T. Shimura C. Shinkai Y*.:
"ATF7IP regulates SETDB1 nuclear localization and increases its ubiquitination"
EMBO Rep. 20:e48297. (2019)
7. Fukuda K, Okuda M, Yusa K*, Shinkai Y*.:
"A CRISPR Knockout Screen Identifies SETDB1-target Retroelement Silencing Factors in Embryonic Stem Cells"
Genome Res. 28:846-858. (2018)
8. Kato M#*, Takemoto K#, Shinkai, Y*.:
"Evidence for a general role of the histone methyltransferase Setdb1 in endogenous retrovirus silencing, not limited to early embryonic cells"
Nat Commun. 9:1683. (2018)
9. Ferry L#. Fournier A#. Tsusaka T#. Adelmant G. Shimazu T. Matano S. Kirsh O. Amouroux R. Dohmae N. Suzuki T. Filion G.J. Deng W. de Dieuleveult M. Lauriane Fritsch L.1, Kudithipudi S. Jeltsch A. Leonhardt H. Hajkova P. Marto J.A. Arita K. Shinkai Y*. Defossez P-A*.:
"Methylation of DNA Ligase 1 by G9a/GLP recruits UHRF1 to replicating DNA and regulates DNA methylation"
Mol Cell 67:550-565.e5. (2017)
10. Shirai A#. Kawaguchi T#. Shimojo H. Muramatsu D. Ishida-Yonetani M. Nishimura Y. Kimura H. Nakayama J*. Shinkai Y*.:
"Impact of nucleic acid and methylated H3K9 binding activities of Suv39h1 on its heterochromatin assembly"
Elife 6:e25317. (2017)