Centers & Labs

RIKEN Brain Science Institute

Laboratory for Molecular Mechanisms of Thalamus Development

Laboratory Head: Tomomi Shimogori (Ph.D.)
Tomomi  Shimogori(Ph.D.)

Diencephalon, contains developing thalamus and hypothalamus, make direct connection to the neocortex, hippocampus and amygdala, respectively, and known to function to maintain higher order cognition and homeostasis. In later developmental time point such as circuit formation stage, it is likely that input from thalamus and hypothalamus influence postsynaptic neurons and change their gene expression, cell survival and dendrite formation by neuronal activity.
To understand how thalamus and hypothalamus can control correct circuit formation and control animals behavior, we are currently focusing on following three projects. First, we use mouse somatosensory barrel cortex which development is controlled by thalamic axon innervation, to reveal molecular mechanism of postsynaptic neuron development. Next, we study molecular mechanism of brain dysfunction in developing hypothalamus, which is triggered by maternal separation. At last, we use common marmoset brain to test gene expression, which is different with mouse cortex, thalamus and hypothalamus to understand mechanism of higher function brain evolution.

Research Subjects

  • Role of thalamocortical axons on thalamocortical circuit development.
  • Effect of maternal separation on hypothalamic development and behaviour.
  • Molecular mechanism of higher functional brain development in marmoset.

Selected Publications

  1. Matsui A, Tran M, Yoshida AC, Kikuchi SS, U M, Ogawa M, Shimogori T.:
    "BTBD3 controls dendrite orientation toward active axons in mammalian neocortex."
    Science. 342 (6162):1114-8. doi: 10.1126/science.1244505. (2013)
  2. Mashiko H, Yoshida AC, Kikuchi SS, Niimi K, Takahashi E, Aruga J, Okano H, Shimogori T.:
    "Comparative anatomy of marmoset and mouse cortex from genomic expression."
    J Neurosci. 32:5039-53. (2012)
  3. Matsui A, Yoshida AC, Kubota M, Ogawa M and Shimogori T.:
    "Mouse in utero electroporation: Controlled spatio-temporal gene transefection."
    J Vis Exp. 54 pii: 3024. doi: 10.3791/3024. (2011)
  4. Yuge K, Kataoka A, Yoshida AC, Itoh D, Aggarwal M, Mori S, Blackshaw S, Shimogori T.:
    "Region-specific expression in early postnatal mouse thalamus."
    J Comp Neurol. 519; 544-61. (2011)
  5. Suzuki-Hirano A, Ogawa M, Kataoka A, Yoshida AC, Itoh D, Ueno M, Blackshaw S, Shimogori T.
    "Dynamic spatiotemporal gene expression in embryonic mouse thalamus."
    J Comp Neurol. 519; 528-43. (2011)
  6. Blackshaw S, Scholpp S, Placzek M, Ingraham H, Simerly R, Shimogori T.:
    "Molecular pathways controlling development of thalamus and hypothalamus: from neural specification to circuit formation."
    J Neurosci. 30:14925-30. (2010)
  7. Shimogori T, Lee DA, Miranda-Angulo A, Yang Y, Jiang L, Yoshida AC, Kataoka A, Mashiko H, Avetisyan M, Qi L, Qian J, and Blackshaw S.:
    "A genomic atlas of mouse hypothalamic development."
    Nat Neurosci. 13:767-75. (2010)
  8. Kataoka A and Shimogori T.:
    "FGF8 controls regional identity in the developing thalamus."
    Development. 135; 2873-81 (2008)

Lab Members

Principal Investigator

Tomomi Shimogori
Laboratory Head

Core Members

Asuka Matsui
Research Scientist
Miyako Hirabayashi
Research Scientist
Nagatoki Kinoshita
Research Scientist
Yurie Maeda
Junior Research Associate
Hiromi Mashiko
Technical Staff I
Yoshiaki Kita
Research Scientist
Mami U
Technical Staff I
Aya Yoshida
Technical Staff II
Satomi Kikuchi
Technical Staff II
Masae Sato
Technical Staff II
Ayumi Abe

Contact information

2-1 Hirosawa, Wako, Saitama 351-0198, Japan

Email: tshimogori [at]

Recent Research Results