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Chromosome Dynamics Laboratory
(Theoretical Biology Laboratory)
RIKEN 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
2000-2004 B.Sc. School of Science, Nagoya University
2004-2006 M.Sc. Department of Physics, Graduate School of Science, Nagoya University
2006-2012 Ph.D. Department of Computational Science and Engineering,
Graduate School of Engineering, Nagoya University
April 2012 - September 2012 Part-time lecturer, Meijo University
April 2012 - Present Research fellow, Theoretical Biological Physics Laboratory Sasai Group, Nagoya University
April 2018 - Present Visiting researcher,Chromosome Dynamics Laboratory (Theoretical Biology Laboratory), RIKEN
Gene expression is controlled in a time and tissue-specific manner in a nucleus of
eukaryotic cells. In such a regulation, gene regulatory elements such as enhancers and
insulators have an important function. Recently, the three-dimensional structure of
DNA and chromosome in that function has been elucidated using the chromosome
conformation capture (3C)-based method. In addition, the three-dimensional structure
of all chromosomes, in other words the genome, in a yeast or human nucleus has been
inferred. However, it is not well understood how these structures and structure
fluctuations affect gene expression on a cell nucleus scale. We are approaching this problem
using a molecular modeling and simulation based on the physical properties of DNA and chromosome.
- Heterogeneous spatial distribution of transcriptional activity in budding yeast nuclei,
Naoko Tokuda and Masaki Sasai, Biophysical Journal,112, 491-504 (2017).
- Dynamical Modeling of Three-Dimensional Genome Organization in Interphase Budding Yeast,
Naoko Tokuda, Tomoki P. Terada, and Masaki Sasai, Biophysical Journal,102, 296-304 (2012).
- Roles of DNA looping in enhancer-blocking activity,
Naoko Tokuda, Masaki Sasai, and George Chikenji, Biophysical Journal,100, 126-134 (2011).
- Crystal Field Wave Functions of CexLa1-xRhIn5, N. Tokuda, T. Nishioka, G.F. Chen, K. Deguchi, K. Kodama, and N.K. Sato,
Journal of the Physical Society of Japan,76, 014706-1-014706-4 (2007).
List of publications
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Page last updated: May 27, 2018