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Division of Molecular and Cellular Biology

1. Member

Staff

Tetsuro Kokubo
Professor.
Graduated from the University of Tokyo with a Ph.D.degree (1990).
Postdoctoral fellow at National Institutes of Health, USA (1990-1995).
Associate professor at Nara Institute of Science and Technology
(1995-2001).
Professor at Yokohama City University (2001-).

Tadashi Wada
Associate Professor.
Graduated from the University of Tokyo with a Ph.D.degree (1992).
Assistant Professor at Tokyo Institute of Technology (1994-2001).
Associate Professor at Tokyo Institute of Technology (2001-2008).
Associate Professor at Yokohama City University (2010-).

Naoki Takai
Assistant Professor.
Graduated from Nagoya University with a Ph.D.degree (2007).
Post-doctoral fellow at Nagoya University (2007-2011).
Assistant Professor at Yokohama City University (2011-).

Postdoc
Yoshifumi Ohyama

Graduate student
Shota Hirama
Shou Takeda
Honami Arai
Keisuke Iwahori
Kanako Moro
Makoto Yabe
Miho Yamaoka
Kiyotaka Yonehara
Kensuke Sakurai

Technical staff
Ryohei Takata
Kiyoshi Watanabe
Kazuyo Teshima

Guest researcher
Koji Kasahara

2. Research

2-1. Functional analysis of TFIID subunits (TAFs)
The regulatory mechanisms that govern gene expression are of fundamental
importance for understanding the normal processes of various biological
phenomena, including development, differentiation and morphogenesis as
well as for deciphering the molecular basis of various genetic
disorders. The general transcription factor TFIID, which is comprised
of TBP and a series of TAFs, plays a central role in the assembly of the
preinitiation complex as well as in the response to transcriptional
activators. We are currently focusing on the characterization of TAF
function, which is essential for these two molecular events, using
budding yeast as our model organism.

2-2. Molecular mechanisms of transcription and translation
Various methods have been developed to address the molecular mechanisms of
essential reactions in living organisms. I am combining methods in biochemistry and
molecular biology, especially by developing in vitro transcription and translation
reactions containing recombinant proteins and/or highly purified factors. In addition,
molecular probes, such as low molecular weight compounds and antibodies that
can neutralize the activities of a target molecule, are often employed in in vitro analyses.
This is one of features of the present study.

3. Recent publications

(Tetsuro Kokubo)

Kasahara K, Ohyama Y, Kokubo T
Hmo1 directs pre-initiation complex assembly to an appropriate site on its target
gene promoters by masking a nucleosome-free region.
Nucleic Acids Res. 2011 May;39(10):4136-50. Epub 2011 Feb 2.

Sugihara F, Kasahara K, Kokubo T
Highly redundant function of multiple AT-rich sequences as core promoter elements
in the TATA-less RPS5 promoter of Saccharomyces cerevisiae.
Nucleic Acids Res. 2011 Jan 1;39(1):59-75. Epub 2010 Aug 30.

Ohyama Y, Kasahara K, Kokubo T
Saccharomyces cerevisiae Ssd1p promotes CLN2 expression by binding to the
5'-untranslated region of CLN2 mRNA.
Genes Cells. 2010 Dec;15(12):1169-88.
doi: 10.1111/j.1365-2443.2010.01452.x. Epub 2010 Oct 26.

Ohtsuki K, Kasahara K, Shirahige K, Kokubo T
Genome-wide localization analysis of a complete set of Tafs reveals a specific effect
of the taf1 mutation on Taf2 occupancy and provides indirect evidence for different
TFIID conformations at different promoters.
Nucleic Acids Res. 2010 Apr 1;38(6):1805-20. Epub 2009 Dec 21.

Takahashi H, Kasahara K, Kokubo T
Saccharomyces cerevisiae Med9 comprises two functionally distinct domains that play
different roles in transcriptional regulation.
Genes Cells. 2009 Jan;14(1):53-67. Epub 2008 Dec 11.

Kasahara K, Ki S, Aoyama K, Takahashi H, Kokubo T.
Saccharomyces cerevisiae HMO1 interacts with TFIID and participates in
start site selection by RNA polymerase II.
Nucleic Acids Res. 2008 Mar;36(4):1343-57. Epub 2008 Jan 10.

(Tadashi Wada)

Taneda T, Zhu W, Cao Q, Watanabe H, Yamaguchi Y, Handa H, Wada T.
Erythropoiesis is regulated by the transcription elongation factor Foggy/Spt5
through gata1 gene regulation.
Genes Cells. 2011 Feb;16(2):231-42.
doi: 10.1111/j.1365-2443.2010.01481.x. Epub 2011 Jan 4.

Kim S, Yamamoto J, Chen Y, Aida M, Wada T, Handa H, Yamaguchi Y.
Evidence that cleavage factor Im is a heterotetrameric protein complex
controlling alternative polyadenylation.
Genes Cells. 2010 Sep 1;15(9):1003-13. Epub 2010 Jul 29.

Hara M, Mori M, Wada T, Tachibana K, Kishimoto T.
Start of the embryonic cell cycle is dually locked in unfertilized starfish eggs.
Development. 2009 May;136(10):1687-96. Epub 2009 Apr 15.

Ando K, Hirao S, Kabe Y, Ogura Y, Sato I, Yamaguchi Y, Wada T, Handa H.
A new APE1/Ref-1-dependent pathway leading to reduction of NF-kappaB and
AP-1, and activation of their DNA-binding activity.
Nucleic Acids Res. 2008 Aug;36(13):4327-36. Epub 2008 Jun 27.

Yoshida M, Kabe Y, Wada T, Asai A, Handa H.
A new mechanism of 6-((2-(dimethylamino)ethyl)amino)-3-hydroxy-7H-
indeno(2,1-c)quinolin-7-one dihydrochloride (TAS-103) action discovered by
target screening with drug-immobilized affinity beads.
Mol Pharmacol. 2008 Mar;73(3):987-94. Epub 2007 Dec 18.

Zhu W, Wada T, Okabe S, Taneda T, Yamaguchi Y, Handa H.
DSIF contributes to transcriptional activation by DNA-binding activators by
preventing pausing during transcription elongation.
Nucleic Acids Res. 2007;35(12):4064-75. Epub 2007 Jun 12.

(Naoki Takai)

Taniguchi Y, Takai N, Katayama M, Kondo T, Oyama T.
Three major output pathways from the KaiABC-based oscillator cooperate to generate robust
circadian kaiBC expression in cyanobacteria.
Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):3263-8. Epub 2010 Jan 28.

Taniguchi Y, Katayama M, Ito R, Takai N, Kondo T, Oyama T.
labA: a novel gene required for negative feedback regulation of the cyanobacterial circadian
clock protein KaiC.
Genes Dev. 2007 Jan 1;21(1):60-70.


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Lastupdated@2012/04/15