Researcher Information

Shinya Takahata

Assistant Professor

Gene Expression & Chromatin Dynamics

Department of Chemistry, Organic and Biological Chemistry


Understanding the mechamnims of chromatin structure regulation and gene expression

FieldMolecular Biology, Epigenetics, Molecular genetics, Biochemistry
KeywordFission yeast, Budding yeast, Gene, Chromosome, Chromatin, Nucleosome, Transcription, Heterochromatin

Introduction of Research

Genome contains numerous number of genes in eukaryote cells. Although there are 5000~ genes coded in yeast genome and 26000~ genes in human genome, all of genes are not equally expressed in cells. It depends on the situation in which the cells are placed. Gene expression is tightly regulated at several stages in living cells, and the landscape of gene expression pattern determines the cellular trait. Various factors are involved in this gene expression regulation, but the most important factor is a structural change of higher order conformation of chromatin. Gene expression is strongly repressed in a dense region of the chromatin structure on the genome, and gene expression is induced in a sparse region of the chromatin structure. Although it has been elucidated that it is a posttranslational chemical modification of histone protein to determine the sparseness and denseness of this chromatin structure, biological molecular reactions followed by the chemical modification at hitone tail is still obscure. The aim of our research is to determine biological supramolecules (proteins, RNA, and signaling chemicals) involved in chromatin structure regulation and to understand the mechanism for gene expression after transformation of chromatin structure at the molecular level.

Heterochromatin: HP1 (Heterochromatin Protein 1) works as a reader protein of H3K9me (Methylated histone H3K9) mediating the condensation of nucleosomes. But the detail of nucleosome condensation mechanism is poorly understood.
Euchromatin: Both of H3K4me and H3K9, 14Ac are observed in this sparse chromatin. But the transcriptional regulation mechanisms (i.e. Transcriptional initiation, elongation and termination) are poorly understood.
Fission yeast strain visualizing the gene expression state with red pigment. Red colony is in a state where gene expression is repressed by heterochromatin, and white colony is in a state in which gene expression is activated by euchromatin. PEV (Position Effect Variegation) indicated by fission yeast strain B is considered to be a proof of the potential diversity conserved in higher organisms.

Representative Achievements

H3K36 methylation state and associated silencing mechanisms. Suzuki S, Murakami Y, Takahata S., Transcription. 2017, 26-31.
Histone H3K36 trimethylation is essential for multiple silencing mechanisms in fission yeast. Suzuki S, Kato H, Suzuki Y, Chikashige Y, Hiraoka Y, Kimura H, Nagao K, Obuse C, Takahata S, Murakami Y., Nucleic Acids Res. 2016, 44(9):4147-4162.
The E2F functional analogue SBF recruits the Rpd3(L) HDAC, via Whi5 and Stb1, and the FACT chromatin reorganizer, to yeast G1 cyclin promoters. Takahata S, Yu Y, Stillman DJ.,EMBO J. 2009, ;28(21), :3378-3389. (F1000 selected)
yFACT induces global accessibility of nucleosomal DNA without H2A-H2B displacement. Xin H, Takahata S, Blanksma M, McCullough L, Stillman DJ, Formosa T., Mol Cell. 2009, 35(3):365-376.
FACT and Asf1 regulate nucleosome dynamics and coactivator binding at the HO promoter. Takahata S, Yu Y, Stillman DJ., Mol Cell. 2009, 34(4), 405-415.

Related industries

Academic degreePh.D.
Self Introduction

How genetic information is extracted from genome packaged in chromatin? It is a big mystery for our mankind. I am studying the molecular system that extracts genetic information from chromatin.

Academic background1993-1997 Faculty of Engineering, Kobe University B.E.
1997-1999 Biochemical Laboratory, SARAYA co. Ltd. Research Fellow
1999-2001 Division of Biological Science, Nara Institute of Science and Technology, M.S.
2001-2004 Graduate School of Integrated Science, Yokohama City University Ph.D.
2004-2005 Graduate School of Integrated Science, Yokohama City University PosDoc
2005-2009 School of Medicine, Univeristy of Utah, USA PosDoc
2009- current position
Affiliated academic societyThe Molecular Biology Society of Japan, The Japan Society of Epigenetics
Room addressFaculty of Science, Building#2 2-203