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Laboratory for Synthetic Biology

Hiroki Ueda


Group Director

Hiroki Ueda (M.D., Ph.D.)

Hiroki Ueda of RIKEN

Original HP

A paradigm sift in biological research from reductionistic to synthetic approach has been undertaken in recent years. Even though the synthetic approach has been acknowledged as a central strategy of life science over the next few decades, basic technologies required in the synthetic approach, such like designing, controlling and manipulating biological molecules (DNAs, proteins and lipids) is remained to be established. The main tasks for laboratory for synthetic biology are to develop basic technologies for synthetic biology through close collaborative study within this center and to present pioneer studies in this new field.

Research Topics

  • Design of chemicals that can control and create dynamic protein behaviour.
  • Design of molecular interactions in circadian clocks.
  • Development of high-throughput genome engineering system.
  • Gene synthesis for the design and construction of biological systems.
  • Design and measurement of protein network dynamics at a single-cell level

Selected Publications

  • Susaki, E.A., Ukai, H. & Ueda, H.R.
    "Next-generation mammalian genetics toward organism-level systems biology"
    npj Systems Biology and Applications 3, Article number: 15 (2017)
  • Ode, K. L., Ukai, H., Susaki, E. A., Narumi, R., Matsumoto, K., Hara, J., et al.
    "Knockout-Rescue Embryonic Stem Cell-Derived Mouse Reveals Circadian-Period Control by Quality and Quantity of CRY1"
    Molecular Cell 65, 176-190 (2017) doi:10.1016/j.molcel.2016.11.022
  • Narumi, R., Shimizu, Y., Ukai-Tadenuma, M., Ode, K. L., Kanda, G. N., Shinohara, Y., et al.
    "Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins"
    Proc. Natl. Acad. Sci. U.S.A. 113, E3461-E3467 (2016) doi:10.1073/pnas.1603799113
  • Tatsuki, F., Sunagawa, G. A., Shi, S., Susaki, E. A., Yukinaga, H., Perrin, D., et al.
    "Involvement of Ca2+-Dependent Hyperpolarization in Sleep Duration in Mammals"
    Neuron 90, 70-85 (2016) doi:10.1016/j.neuron.2016.02.032
  • Sunagawa, G.A., Sumiyama, K., Ukai-Tadenuma, M., Perrin, D. et al.
    "Mammalian Reverse Genetics without Crossing Reveals Nr3a as a Short-Sleeper Gene"
    Cell Reports 14, 662-677 (2016) doi:10.1016/j.celrep.2015.12.052
  • Susaki, E. A. & Ueda, H. R.
    "Whole-body and Whole-Organ Clearing and Imaging Techniques with Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals"
    Cell Chemical Biology 23, 137-157 (2016) doi:10.1016/j.chembiol.2015.11.009
  • Susaki, E. A., Tainaka, K., Perrin, D., Yukinaga, H., Kuno, A. & Ueda, H. R.
    "Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging"
    Nat. Protoc. 10, 1709-1727 (2015) doi:10.1038/nprot.2015.085
  • Tainaka, K., Kubota, S. I., Suyama, T. Q., Susaki, E. A., Perrin, D., Ukai-Tadenuma, M., et al.
    "Whole-Body Imaging with Single-Cell Resolution by Tissue Decolorization"
    Cell 159, 911-924 (2014) doi:10.1016/j.cell.2014.10.034
  • Jolley, C. C., Ukai-Tadenuma, M., Perrin, D. & Ueda, H. R.
    "A Mammalian Circadian Clock Model Incorporating Daytime Expression Elements"
    Biophys. J. 107, 1462-1473 (2014) doi:10.1016/j.bpj.2014.07.022
  • Susaki, E. A., Tainaka, K., Perrin, D., Kishino, F., Tawara, T., Watanabe, T. M., et al.
    "Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis"
    Cell 157, 726-739 (2014) doi:10.1016/j.cell.2014.03.042