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Epigenetics Drug Discovery Unit _Publication List

Epigenetics Drug Discovery Unit

1

Crystal structure of eukaryotic translation initiation factor 2B

Kashiwagi K, Takahashi M, Nishimoto M, Hiyama TB, Higo T, Umehara T, Sakamoto K, Ito T, Yokoyama S
Nature, 351(7592), 122-125 (2016).
2

Distribution of histone H4 modifications as revealed by a panel of specific monoclonal antibodies

Hayashi-Takanaka Y, Maehara K, Harada A, Umehara T, Yokoyama S, Obuse C, Ohkawa Y, Nozaki N, Kimura H
Chromosome Res, 23(4), 753-766 (2015).
3

Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation

Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S.
Sci Rep, 5, 17204 (2015).
4

Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT.

Tochio N, Umehara T, Nakabayashi K, Yoneyama M, Tsuda K, Shirouzu M, Koshiba S, Watanabe S, Kigawa T, Sasazuki T, Shirasawa S, Yokoyama S.
J Struct Funct Genomics, 16(2), 55-65 (2015).
5

Lysine-specific demethylase LSD2 suppresses lipid influx and metabolism in hepatic cells.

Nagaoka K, Hino S, Sakamoto A, Anan K, Takase R, Umehara T, Yokoyama S, Sasaki Y, Nakao M.
Mol Cell Biol, 35(7), 1068-1080 (2015).
6

New frontiers of epigenetics researches in pharmaceutical sciences.

Umehara T, Hori Y.
Yakugaku Zasshi, 135(1), 1-2 (2015).
7

Development of a hexahistidine-3× FLAG-tandem affinity purification method for endogenous protein complexes in Pichia pastoris.

Higo T, Suka N, Ehara H, Wakamori M, Sato S, Maeda H, Sekine S, Umehara T, Yokoyama S.
J Struct Funct Genomics, 15(4), 191–199 (2014).
8

Expanded genetic code technologies for incorporating modified lysine at multiple sites.

Yanagisawa T, Umehara T, Sakamoto K, Yokoyama S.
Chembiochem, 15(15), 2181-2187 (2014).
9

Multiple site-specific installations of Nε-monomethyl-L-lysine into histone proteins by cell-based and cell-free protein synthesis.

Yanagisawa T, Takahashi M, Mukai T, Sato S, Wakamori M, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S.
ChemBioChem, 15(12), 1830-1838 (2014).
10

Structures of histone methyltransferase SET7/9 in complexes with adenosylmethionine derivatives.

Niwa H, Handa N, Tomabechi Y, Honda K, Toyama M, Ohsawa N, Shirouzu M, Kagechika H, Hirano T, Umehara T, Yokoyama S.
Acta Crystallogr D Biol Crystallogr, 69(Pt4), 595-602 (2013).
11

FAD-dependent lysine-specific demethylase-1 regulates cellular energy expenditure.

Hino S, Sakamoto A, Nagaoka K, Anan K, Wang Y, Mimasu S, Umehara T, Yokoyama S, Kosai K, Nakao M.
Nat Commun, 3, 758 (2012).
12

A tandem insertion vector for large-scale preparation of nucleosomal DNA.

Wakamori M, Umehara T, Yokoyama S.
Anal Biochem, 423(1), 184-186 (2012).
13

Genetic-code evolution for protein synthesis with non-natural amino acids.

Mukai T, Yanagisawa T, Ohtake K, Wakamori M, Adachi J, Hino N, Sato A, Kobayashi T, Hayashi A, Shirouzu M, Umehara T, Yokoyama S, Sakamoto K.
Biochem Biophys Res Commun, 411(4), 757-761 (2011).
14

Real-time imaging of histone H4K12-specific acetylation determines the modes of action of histone deacetylase and bromodomain inhibitors.

Ito T, Umehara T, Sasaki K, Nakamura Y, Nishino N, Terada T, Shirouzu M, Padmanabhan B, Yokoyama S, Ito A, Yoshida M.
Chem Biol, 18(4), 495-507 (2011).
15

Crystallographic study of a site-specifically cross-linked protein complex with a genetically incorporated photoreactive amino acid.

Sato S, Mimasu S, Sato A, Hino N, Sakamoto K, Umehara T, Yokoyama S.
Biochemistry, 50(2), 250-257 (2011).
16

Cell-permeable carboxyl-terminal p27(Kip1) peptide exhibits anti-tumor activity by inhibiting Pim-1 kinase.

Morishita D, Takami M, Yoshikawa S, Katayama R, Sato S, Kukimoto-Niino M, Umehara T, Shirouzu M, Sekimizu K, Yokoyama S, Fujita N.
J Biol Chem, 286(4), 2681-2688 (2011).
17

Structural insight into the zinc finger CW domain as a histone modification reader.

He F, Umehara T, Saito K, Harada T, Watanabe S, Yabuki T, Kigawa T, Takahashi M, Kuwasako K, Tsuda K, Matsuda T, Aoki M, Seki E, Kobayashi N, Güntert P, Yokoyama S, Muto Y.
Structure, 18(9), 1127-1139 (2010).
18

Structural implications for K5/K12-di-acetylated histone H4 recognition by the second bromodomain of BRD2.

Umehara T, Nakamura Y, Wakamori M, Ozato K, Yokoyama S, Padmanabhan B.
FEBS Lett, 584(18), 3901-3908 (2010).
19

Structurally designed trans-2-phenylcyclopropylamine derivatives potently inhibit histone demethylase LSD1/KDM1.

Mimasu S, Umezawa N, Sato S, Higuchi T, Umehara T, Yokoyama S.
Biochemistry, 49(30), 6494-6503 (2010).
20

A series of bacterial co-expression vectors with rare-cutter recognition sequences.

Wakamori M, Umehara T, Yokoyama S.
Protein Expr Purif, 74(1), 88-98 (2010).
21

Solution structure of histone chaperone ANP32B: interaction with core histones H3-H4 through its acidic concave domain.

Tochio N, Umehara T, Munemasa Y, Suzuki T, Sato S, Tsuda K, Koshiba S, Kigawa T, Nagai R, Yokoyama S.
J Mol Biol, 401(1), 97-114 (2010).
22

Mapping of the basic amino-acid residues responsible for tubulation and cellular protrusion by the EFC/F-BAR domain of pacsin2/Syndapin II.

Shimada A, Takano K, Shirouzu M, Hanawa-Suetsugu K, Terada T, Toyooka K, Umehara T, Yamamoto M, Yokoyama S, Suetsugu S.
FEBS Lett, 584(6), 1111-1118 (2010).
23

Structural basis for acetylated histone H4 recognition by the human BRD2 bromodomain.

Umehara T, Nakamura Y, Jang MK, Nakano K, Tanaka A, Ozato K, Padmanabhan B, Yokoyama S.
J Biol Chem, 285(10), 7610-7618 (2010).
24

ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators.

Kumarevel T, Tanaka T, Umehara T, Yokoyama S.
Nucleic Acids Res, 37(14), 4723-4735 (2009).
25

Solution structure of the extraterminal domain of the bromodomain-containing protein BRD4.

Lin YJ, Umehara T, Inoue M, Saito K, Kigawa T, Jang MK, Ozato K, Yokoyama S, Padmanabhan B, Güntert P.
Protein Sci, 17(12), 2174-2179 (2008).
26

Crystal structures of fission yeast histone chaperone Asf1 complexed with the Hip1 B-domain or the Cac2 C terminus.

Malay AD, Umehara T, Matsubara-Malay K, Padmanabhan B, Yokoyama S.
J Biol Chem, 283(20), 14022-14031 (2008).
27

Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25 A.

Mimasu S, Sengoku T, Fukuzawa S, Umehara T, Yokoyama S.
Biochem Biophys Res Commun, 366(1), 15-22 (2008).
28

Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome.

Nakamura Y, Umehara T, Tanaka A, Horikoshi M, Padmanabhan B, Yokoyama S.
Biochem Biophys Res Commun, 359(3), 503-509 (2007).
29

Solution structure of the zinc finger HIT domain in protein FON.

He F, Umehara T, Tsuda K, Inoue M, Kigawa T, Matsuda T, Yabuki T, Aoki M, Seki E, Terada T, Shirouzu M, Tanaka A, Sugano S, Muto Y, Yokoyama S.
Protein Sci, 16(8), 1577-1587 (2007).
30

Purification, crystallization and preliminary X-ray diffraction of the C-terminal bromodomain from human BRD2.

Umehara T, Wakamori M, Tanaka A, Padmanabhan B, Yokoyama S.
Acta Crystallogr Sect F-Struct Biol Cryst Commun, 63(Pt7), 613-615 (2007).
31

Structural and functional differences of SWIRM domain subtypes.

Yoneyama M, Tochio N, Umehara T, Koshiba S, Inoue M, Yabuki T, Aoki M, Seki E, Matsuda T, Watanabe S, Tomo Y, Nishimura Y, Harada T, Terada T, Shirouzu M, Hayashizaki Y, Ohara O, Tanaka A, Kigawa T, Yokoyama S.
J Mol Biol, 369(1), 222-238 (2007).
32

Purification, crystallization and preliminary X-ray diffraction analysis of the non-ATPase subunit Nas6 in complex with the ATPase subunit Rpt3 of the 26S proteasome from Saccharomyces cerevisiae.

Nakamura Y, Umehara T, Tanaka A, Horikoshi M, Padmanabhan B, Yokoyama S.
Acta Crystallogr Sect F-Struct Biol Cryst Commun, 63(Pt3), 190-192 (2007).
33

Crystal structure of the human BRD2 bromodomain: insights into dimerization and recognition of acetylated histone H4.

Nakamura Y, Umehara T, Nakano K, Jang MK, Shirouzu M, Morita S, Uda-Tochio H, Hamana H, Terada T, Adachi N, Matsumoto T, Tanaka A, Horikoshi M, Ozato K, Padmanabhan B, Yokoyama S.
J Biol Chem, 282(6), 4193-4201 (2007).
34

Crystallization of the archaeal transcription termination factor NusA: a significant decrease in twinning under microgravity conditions.

Tanaka H, Umehara T, Inaka K, Takahashi S, Shibata R, Bessho Y, Sato M, Sugiyama S, Fusatomi E, Terada T, Shirouzu M, Sano S, Motohara M, Kobayashi T, Tanaka T, Tanaka A, Yokoyama S.
Acta Crystallogr Sect F-Struct Biol Cryst Commun, 63(Pt2), 69-73 (2007).
35

Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome.

Nakamura Y, Nakano K, Umehara T, Kimura M, Hayashizaki Y, Tanaka A, Horikoshi M, Padmanabhan B, Yokoyama S.
Structure, 15(2), 179-189 (2007).
36

Crystal structure analysis of the PHD domain of the transcription co-activator Pygopus.

Nakamura Y, Umehara T, Hamana H, Hayashizaki Y, Inoue M, Kigawa T, Shirouzu M, Terada T, Tanaka A, Padmanabhan B, Yokoyama S.
J Mol Biol, 370(1), 80-92 (2007).
37

Global analysis of functional surfaces of core histones with comprehensive point mutants.

Matsubara K, Sano N, Umehara T, Horikoshi M.
Genes Cells, 12(1), 13-33 (2007).
38

Solution structure of the SWIRM domain of human histone demethylase LSD1.

Tochio N, Umehara T, Koshiba S, Inoue M, Yabuki T, Aoki M, Seki E, Watanabe S, Tomo Y, Hanada M, Ikari M, Sato M, Terada T, Nagase T, Ohara O, Shirouzu M, Tanaka A, Kigawa T, Yokoyama S.
Structure, 14(3), 457-468 (2006).
39

Structural similarity between histone chaperone Cia1p/Asf1p and DNA-binding protein NF-kappaB.

Padmanabhan B, Kataoka K, Umehara T, Adachi N, Yokoyama S, Horikoshi M.
J Biochem, 138(6), 821-829 (2005).
40

Purification, crystallization and preliminary X-ray diffraction analysis of the histone chaperone cia1 from fission yeast.

Umehara T, Otta Y, Tsuganezawa K, Matsumoto T, Tanaka A, Horikoshi M, Padmanabhan B, Yokoyama S.
Acta Crystallogr Sect F-Struct Biol Cryst Commun, 61(Pt11), 971-973 (2005).
41

Genome-wide expression analysis of mouse liver reveals CLOCK-regulated circadian output genes.

Oishi K, Miyazaki K, Kadota K, Kikuno R, Nagase T, Atsumi G, Ohkura N, Azama T, Mesaki M, Yukimasa S, Kobayashi H, Iitaka C, Umehara T, Horikoshi M, Kudo T, Shimizu Y, Yano M, Monden M, Machida K, Matsuda J, Horie S, Todo T, Ishida N.
J Biol Chem, 278(42), 41519-41527 (2003).
42

Transcription initiation factor IID-interactive histone chaperone CIA-II implicated in mammalian spermatogenesis

Umehara T, Horikoshi M.
J Biol Chem, 278(37), 35660-35667 (2003).
43

New theory on gene regulation: mechanism of formation of chromosome functional and boundary regions.

Horikoshi M, Yamamoto T, Umehara T, Suzuki T, Adachi N, Kimura A.
Tanpakushitsu Kakusan Koso, 48(3), 205-222 (2003).
44

Chromosomal gradient of histone acetylation established by Sas2p and Sir2p functions as a shield against gene silencing.

Kimura A, Umehara T, Horikoshi M.
Nat Genet, 32(3), 370-377 (2002).
45

Polyanionic stretch-deleted histone chaperone cia1/Asf1p is functional both in vivo and in vitro.

Umehara T, Chimura T, Ichikawa N, Horikoshi M.
Genes Cells, 7(1), 59-73 (2002).
46

Cell death with predominant apoptotic features in Saccharomyces cerevisiae mediated by deletion of the histone chaperone ASF1/CIA1.

Yamaki M, Umehara T, Chimura T, Horikoshi M.
Genes Cells, 6(12), 1043-1054 (2001).
47

Restricted expression of a member of the transcription elongation factor S-II family in testicular germ cells during and after meiosis.

Umehara T, Kida S, Hasegawa S, Fujimoto H, Horikoshi M.
J Biochem, 121(3), 598-603 (1997).
48

Isolation and characterization of a cDNA encoding a new type of human transcription elongation factor S-II.

Umehara T, Kida S, Yamamoto T, Horikoshi M.
Gene, 167(1-2), 297-302 (1995).
49

Isolation of a cDNA encoding a mouse TFIID subunit containing histone H4 homology.

Umehara T, Kida S, Horikoshi M.
Gene, 161(2), 301-302 (1995).
50

Three distinct regions in a rat TFIID subunit containing histone H4 homology.

Kida S, Umehara T, Horikoshi M.
Gene, 161(2), 303-304 (1995).

和文論文

CLST was reorganized into three centers according to the RIKEN 4th Medium-Term Plan from April 1, 2018. For the latest information of Epigenetics Drug Discovery Unit, please visit the following websites.


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