Curriculum Vitae
PERSONAL INFORMATION
Name:

Tomomi Shimogori

Address:

2-1 Hirosawa Wako
Saitama, Japan
phone: 81-48-467-9779;
fax:81-48-467-9763;
e-mail: tshimogori@brain.riken.jp

Education:

B.A. Hoshi Collage of Pharmacy, Tokyo, Japan1993

Ph.D., Pharmaceutical Sciences, Graduate School,Chiba University, Chiba, Japan

1998

ACADEMIC APPOINTMENTS
1998 to 2004
Dept. Neurobiology, Pharmacology and Physiology, Universityof Chicago, USA Laboratory of Dr. Elizabeth A. Grove2004 to 2010
RIKEN BSI Unit Leader of Shimogori Research Unit2010 to present
RIKEN BSI Team Leader of Lab for Molecular Mechanisms ofThalamus Development
PUBLICATIONS
Peer Reviewed Journal Articles
1.

He Y, Shimogori T, Kashiwagi K, Shirahata A, Igarashi K. (1995) Inhibition of cell
growth by combination of alpha-difluoromethylornithine and an inhibitor of spermine
synthase. J Biochem (Tokyo). 117, 824-9.

2.

Igarashi K, Koga K, He Y, Shimogori T, Ekimoto H, Kashiwagi K, Shirahata A.
(1995) Inhibition of the growth of various human and mouse tumor cells by
1,15-bis(ethylamino)-4,8,12-triazapentadecane. Cancer Res. 55, 2615-9.

3.

Shimogori T, Suzuki T, Kashiwagi K, Kakinuma Y, Igarashi K. (1996)
Enhancement of helicase activity and increase of eIF-4E phosphorylation inornithine decarboxylase-overproducing cells. Biochem Biophys Res Commun. 222,748-52.

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4.

Shimogori T, Kashiwagi K, Igarashi K. (1996) Spermidine regulation of protein
synthesis at the level of initiation complex formation of Met-tRNAi, mRNA andribosomes. Biochem Biophys Res Commun. 223, 544-8.

5.

Sakata K, Fukuchi-Shimogori T, Kashiwagi K, Igarashi K. (1997) Protein
Identification of regulatory region of antizyme necessary for the negative regulationof polyamine transport. Biochem Biophys Res Commun. 238, 415-9.

6.

Fukuchi-Shimogori T, Ishii I, Kashiwagi K, Mashiba H, Ekimoto H, Igarashi K.
(1997) Malignant transformation by overproduction of translation initiation factor
eIF4G. Cancer Res. 57, 5041-4.

7.

Shibata M, Shinga J, Yasuhiko Y, Kai M, Miura K, Shimogori T, Kashiwagi K,
Igarashi K, Shiokawa K. (1998) Overexpression of S-adenosylmethionine
decarboxylase (SAMDC) in early Xenopus embryos induces cell dissociation andinhibits transition from the blastula to gastrula stage. Int J Dev Biol. 42, 675-86.

8.

Meksuriyen D, Fukuchi-Shimogori T, Tomitori H, Kashiwagi K, Toida T, Imanari T,Kawai G, Igarashi K. (1998) Formation of a complex containing ATP, Mg2+, andspermine. Structural evidence and biological significance. J Biol Chem. 273,30939-44.

9.

Antognoni F, Del Duca S, Kuraishi A, Kawabe E, Fukuchi-Shimogori T, Kashiwagi
K, Igarashi K. (1999) Transcriptional inhibition of the operon for the spermidine
uptake system by the substrate-binding protein PotD. J Biol Chem. 274, 1942-8.

10. Iwata S, Sato Y, Asada M, Takagi M, Tsujimoto A, Inaba T, Yamada T, Sakamoto
S, Yata J, Shimogori T, Igarashi K, Mizutani S. (1999) Anti-tumor activity ofantizyme which targets the ornithine decarboxylase (ODC) required for cell growthand transformation. Oncogene. 18, 165-72.
11. Hayashi S, Nishimura K, Fukuchi-Shimogori T, Kashiwagi K, Igarashi K. (2000)
Increase in cap- and IRES-dependent protein synthesis by overproduction oftranslation initiation factor eIF4G. Biochem Biophys Res Commun. 277,117-23.
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12. Fukuchi-Shimogori T, Grove EA. (2001) Neocortex patterning by the secreted
signaling molecule FGF8. Science. 294:1071-4.
13. Nishimura K, Ohki Y, Fukuchi-Shimogori T, Sakata K, Saiga K, Beppu T,
Shirahata A, Kashiwagi K, Igarashi K. (2002) Inhibition of cell growth throughinactivation of eukaryotic translation initiation factor 5A (eIF5A) by deoxyspergualin.
Biochem J. 363, 761-8.
14. Grove EA and Fukuchi-Shimogori T. (2003) Development of the vertebrate
forebrain. Ann. Rev. Neurosci. 26, 355-80.
15. Fukuchi-Shimogori T, Grove EA. (2003) Emx2 Patterns the Neocortex byRegulating FGF Positional Signaling. Nat Neurosci. 8, 825-31.
16. Shimogori T., VanSant J, Paik ES, and Grove EA. (2004) Members of the Wnt, Fz,and Frp gene families expressed in postnatal mouse cerebral cortex. J Comp
Neurol. 473, 496-510.
17. Shimogori T., Banuchi V., Ng HY., Strauss JB. and Grove EA. (2004) Embryonicsignaling centers expressing BMP, Wnt and FGF proteins interact to pattern thecerebral cortex. Development. 13,5639-47.
18. Shimogori T and Grove EA. (2005) FGF8 Regulates Neocortical Guidance ofArea-specific Thalamic Innervation. J Neurosci. 13, 6550-60.
19. Sasaki T, Nishihara H, Hirakawa M, Fujimura K, Tanaka M, Kokubo N,
Kimura-Yoshida C, Matsuo I, Sumiyama K, Saitou N, Shimogori T, Okada N.
(2008) Possible involvement of SINEs in mammalian-specific brain formation. Proc
Natl Acad Sci U S A. 105, 4220-5.
20. Shimogori T and Ogawa M. (2008) Gene application with in utero electroporationin mouse embryonic brain. Dev Growth Differ. 50;499-506 (review).

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21. Imayoshi I, Shimogori T, Ohtsuka T and Kageyama R. (2008) Hes genes andneurogenin regulate non-neural versus neural fate specification in the dorsal
telencephalic midline. Development. 135; 2531-41.
22. Kataoka A and Shimogori T. (2008) FGF8 controls regional identity in thedeveloping thalamus. Development. 135; 2873-81
23. Kinameri E, Inoue T, Aruga J, Imayoshi I, Kageyama R, Shimogori T* and Moore
AW*. (2008) Prdm proto-oncogene transcription factor family expression andinteraction with the Notch-Hes pathway in mouse neurogenesis. PLoS ONE.
3:e3859. *corresponding authors
24. Suzuki-Hirano A and Shimogori T. (2009) The role of Fgf8 in telencephalic anddiencephalic patterning. Semin. Cell. Devbiol. 20; 719-725 (review).
25. Fabre P, Shimogori T, Charron F. (2010) Segregation of ipsilateral retinal ganglion
cell axons at the optic chiasm requires the Shh receptor Boc. J Neurosci. 30;
266-75.
26. Aggarwal M, Mori S, Shimogori T, Blackshaw S, Zhang J. (2010) Three
dimentional rapid diffusion tensor microimaging for anatomical characterization andgene expression mapping the mouse brain. Journal Magnetic Resonance inMedicine. 64; 249-261.
27. 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*. (2010) A genomic atlas ofmouse hypothalamic development. Nat Neurosci. 13:767-75. *correspondingauthors.
28. Okada N, Sasaki T, Shimogori T, Nishihara H. (2010) Emergence of mammals byemergency: exaptation. Genes Cells. 15:801-12.

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29. Toyoda R, Assimacopoulos S, Wilcoxon J, Taylor A, Feldman P, Suzuki-Hirano A,Shimogori T, Grove EA. (2010) FGF8 acts as a classic diffusible morphogen topattern the neocortex. Development. 137:3439-48.
30. Blackshaw S, Scholpp S, Placzek M, Ingraham H, Simerly R, Shimogori T. (2010)
Molecular pathways controlling development of thalamus and hypothalamus: fromneural specification to circuit formation. J Neurosci. 30:14925-30. Review.
31. Suzuki-Hirano A, Ogawa M, Kataoka A, Yoshida AC, Itoh D, Ueno M, Blackshaw S,Shimogori T. (2011) Dynamic spatiotemporal gene expression in embryonicmouse thalamus. J Comp Neurol. 519; 528-43.
32. Yuge K, Kataoka A, Yoshida AC, Itoh D, Aggarwal M, Mori S, Blackshaw S,Shimogori T. (2011) Region-specific expression in early postnatal mouse thalamus.
J Comp Neurol. 519; 544-61.
33. Matsui A, Yoshida AC, Kubota M, Ogawa M and Shimogori T. (2011) Mouse inutero electroporation: Controlled spatio-temporal gene transefection. J Vis Exp. 54pii: 3024.
34. Hama H, Kurokawa H, Kawano H, Ando R, Shimogori T, Noda H, Fukami K,Sakaue-Sawano A, Miyawaki A. (2011) Scale: a chemical approach for fluorescenceimaging and reconstruction of transparent mouse brain. Nature Neurosci.
14:1481-8.
35. Chiara F, Badaloni A, Croci L, Yeh ML, Cariboni A, Hoerder-Suabedissen A,Consalez GG, Eickholt B, Shimogori T, Parnavelas JG, Rakić S. (2012) Early B-cellfactors 2 and 3 (EBF2/3) regulate early migration of Cajal-Retzius cells from thecortical hem. Dev Biol. 365:277-89.
36. Mashiko H, Yoshida AC, Kikuchi SS, Niimi K, Takahashi E, Aruga J, Okano H,Shimogori T. (2012) Comparative anatomy of marmoset and mouse cortex fromgenomic expression. J Neurosci. 32:5039-53.

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37. Nakagawa Y, Shimogori T. (2012) Diversity of thalamic progenitor cells andpostmitotic neurons. Eur J Neurosci. 35:1554-62.
38. Nakanishi A, Kobayashi N, Suzuki-Hirano A, Nishihara H, Sasaki T, Hirakawa M,Sumiyama K, Shimogori T, Okada N. (2012) A SINE-derived element constitutes aunique modular enhancer for mammalian diencephalic Fgf8. PLoS One. 7:e43785
39. Huilgol D, Udin S, Shimogori T, Saha B, Roy A, Aizawa S, Hevner RF, Meyer G,Ohshima T, Pleasure SJ, Zhao Y, Tole S. (2013) Dual origins of the mammalianaccessory olfactory bulb revealed by an evolutionarily conserved migratory stream.
Nat Neurosci. doi: 10.1038/nn.3297.
40. Kumagai A, Ando R, Miyatake H, Greimel P, Kobayashi T, Hirabayashi Y,Shimogori T, Miyawaki A. (2013) A bilirubin-inducible fluorescent protein from eelmuscle. Cell. 153:1602-11.
41. Matsui A, Tran M, Yoshida AC, Kikuchi SS, U M, Ogawa M, Shimogori T. (2013)
BTBD3 controls dendrite orientation toward active axons in mammalian neocortex.
Science. 342 (6162):1114-8. doi: 10.1126/science.1244505.
42. Forni PE, Bharti K, Flannery EM, Shimogori T, and Wray S. (2013) The Indirect
Role of Fibroblast Growth Factor-8 in Defining Neurogenic Niches of theOlfactory/GnRH Systems. J Neurosci. 33:19620-19634
43. Yamanaka T, Tosaki A, Kurosawa M, Matsumoto G, Koike M, Uchiyama Y, Maity
SN, Shimogori T, Hattori N, Nukina N. (2014) NF-Y inactivation causes atypicalneurodegeneration characterized by ubiquitin and p62 accumulation andendoplasmic

reticulum

disorganization.

NatCommun.

5:3354.

doi:

10.1038/ncomms4354.
44. Golding B, Pouchelon G, Bellone C, Murthy S, Di Nardo AA, Govindan S, Ogawa M,
Shimogori T, Lüscher C, Dayer A, Jabaudon D. (2014) Retinal input directs therecruitment of inhibitory interneurons into thalamic visual circuits. Neuron.
81(5):1057-69. doi: 10.1016/j.neuron.2014.01.032.
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45. Yamanaka T, Wong HK, Tosaki A, Bauer PO, Wada K, Kurosawa M, Shimogori T,Hattori N, Nukina N. (2014) Large-scale RNA interference screening in m PLoS One.
2014 Apr 4;9(4):e93891. doi: 10.1371/journal.pone.0093891.
46. Caballero IM, Manuel MN, Molinek M, Quintana-Urzainqui I, Mi D, Shimogori T,Price DJ. (2014) Cell-autonomous repression of shh by transcription factor pax6
regulates diencephalic patterning by controlling the central diencephalic organizer.
Cell Rep. 2014 Sep 11;8(5):1405-18. doi: 10.1016/j.celrep.2014.07.051.
47. Kurosawa M, Matsumoto G, Kino Y, Okuno M, Kurosawa-Yamada M, Washizu C,Taniguchi H, Nakaso K, Yanagawa T, Warabi E, Shimogori T, Sakurai T, Hattori N,Nukina N. (2015) Depletion of p62 reduces nuclear inclusions and paradoxicallyameliorates disease phenotypes in Huntington's model mice. Hum Mol Genet.
24(4):1092-105. doi: 10.1093/hmg/ddu522.
48. Miyazaki H, Oyama F, Inoue R, Aosaki T, Abe T, Kiyonari H, Kino Y, Kurosawa M,Shimizu J, Ogiwara I, Yamakawa K, Koshimizu Y, Fujiyama F, Kaneko T, Shimizu
H, Nagatomo K, Yamada K, Shimogori T, Hattori N, Miura M, Nukina N. (2015)!
Singular localization of sodium channel β4 subunit in unmyelinated fibres and its
role in the striatum.

Nat Commun. 5:5525. doi: 10.1038/ncomms6525.!

49. Liu J, Merkle FT, Gandhi AV, Gagnon JA, Woods IG, Chiu CN, Shimogori T,Schier AF, Prober DA. (2015) Evolutionarily conserved regulation of hypocretin
neuron specification by Lhx9. Development. 2015 Feb 27. pii: dev.117424.

Book Chapters
1.

Shimogori T and Grove EA. (2006) Subcortical and Neocortical Guidance of
Area-specific Thalamic innervation: Development and Plasticity in sensory
thalamus and cortex, Eds: Erzurumlu, R., Guido, W., Molnar, Z., Springer,Heidelberg. P68

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2.

Shimogori T. (2006) Micro In Utero Electroporation for Efficient Gene Targeting inMouse Embryos, In: Gene Transfer, Eds: Friedmann T. and Rossi J., Cold Spring
Harbor, Laboratory Press, p427

3.

Shimogori T and Ogawa M. (2008) Practical application of micro electroporation
into developing mouse brain. Springer. P153-167.

INVITED PRESENTATIONS
1. Japanese Society of Developmental Biology, Sendai, Japan (2004)
2. Society of Evolution Studies, Kyoto, Japan (2007)
3. The Japanese Society of Child Neurology, Osaka, Japan (2007)

4. Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada (2008)
5. Johns Hopkins Medical Institute Research Seminar, Baltimore, USA (2008)
6. Biochemistry and molecular biology, Kobe, Japan (2008)
7. University Miguel Hernandez, Alicante, Spain (2009)
8. Invited speaker, Barrel XXII satellite meeting (2009. Oct)
9. Neuroscience at the University of Chicago, Chicago, USA (2009)
10. Institute of neuroscience (ION), Shinghai, China (2009. Nov)
11. Pekin University, Beijing, China (2009. Nov)
12. The 8th Binneal Chinese Neuroscience meting, Guangzhou, China (2009. Nov)
13. Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada (2010. May)
14. Department of physiology, anatomy and genetics, Oxford (2010. June)
15. Department of biological science, Sheffield, UK (2010. June)
16. Research department of cell and developmental biology, University of CollegeLondon, UK (2010. June)
17. FAONS Congress-2010, Lucknow, India (2010, Nov)
18. SFN mini symposium (molecular pathways controlling development of thalamus andhypothalamus: from neural specification to circuit formation), DC, USA(2010 Nov)
19. Neurobiology Section, Biological Sciences Division, University of California, San
Diego (2010 Nov)
20. Development and Plasticity of Thalamocortical Systems, Arolla, Switzerland (2011.
Feb)
21. Johns Hopkins Medical Institute Research Seminar, Baltimore, USA (2011. Nov)
22. Neural development; Stem cell perspective, Japan (2012 Jan)
23. Research department of cell and developmental biology, University of College London,UK (2013 Jan)
24. Cortex club speaker, Oxford, UK (2013 Jan)
25. Salk institute for biological studies, USA (2013 Jan)

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26. IBRO Lecture course, Hong Kong (2013 June)
27. ANS2013 (Australian Neuroscience meeting), Melbourne (2013 Jan)
28. Gordon Research Conference (Dendrites: molecules, structure and function),
Les Diablerets, Switzerland (2013 May)
29. Geneva neuroscience center, University of Geneva, Switzerland (2013 May)
30. Yale University School of Medicine, New Haven USA. (2013 Nov)
31. Japanese Conference for Laboratory Animal Science and Technology, Sapporo, Japan(2014 May)
32. Gordon Research Conference (Molecular and Cellular Neurobiology), The Hong KongUniversity of Science and Technology, Hong Kong (2014 July)
33. INCF 2014, Leiden, Netherland (2014 Aug)
34. Erasmus University Rotterdam, Rotterdam, Netherland (2014 Aug)TEACHING EXPERIENCE
1.

Tokyo University graduate school (2005)

2.

The 8th IBRO school on Neuroscience at the Tata Institute of Fundamental
Research, Mumbai, India (2006)

3.

BSI tutorial lecture (Neural Development) (2006)

4.

BSI tutorial lecture (Neural Development) (2007)

5.

Tokyo Metropolitan University (2008)

6.

The IBRO-AORC Associate School, Nanjing, China (2009)

7.

Tokyo Medical and Dental University (2009)8.

Tokyo Metropolitan University (2010)

9.

Tokyo University (2011)10.

The IBRO school in Neuroscience at the Hong Kong University, Hong Kong

(2012)
Representative Abstracts and Oral Presentations
1.

Seth Blackshaw, Aya C Yoshida, Ayane Kataoka, Dan Lee, Ana Miranda-Angulo,
Lizhi Jiang, Marina Avetisyan, Lixin Qi, and Tomomi Shimogori. Genomicanalysis of mouse hypothalamic development (1). 40th Annual Meeting of theSociety for Neuroscience, Chicago (2009.Oct).

2.

Tomomi Shimogori, Aya Yoshida, Ayane Kataoka, Dan Lee, Ana Miranda-Angulo,
Lizhi Jiang, Marina Avetisyan, Lixin Qi, andSeth Blackshaw. Genomic analysis of9Curriculum Vitae
mouse hypothalamic development (2). 40th Annual Meeting of the Society forNeuroscience, Chicago (2009.Oct).
3.

Kazuya Yuge, Aya C Yoshida, Satomi Kikuchi, Tomomi Shimogori. Gene
expression in the barrel cortex triggered by thalamocortical innervation. 40thAnnual Meeting of the Society for Neuroscience, Chicago (2009.Oct).

4.

Asuka Suzuki-Hirano and Tomomi Shimogori. Comparative analysis of chick andmouse developing epithalamus. International Conference, “Construction andreconstruction of the brain”. Awaji, Japan (2009. Oct).

5.

Asuka Suzuki-Hirano and Tomomi Shimogori. Comparative analysis of chick andmouse developing epithalamus. Japanese Society of Developmental Biologists.
Niigata, Japan (2009. May).

6.

Kazuya Yuge, Aya C Yoshida, Ayane Kataoka, Seth Blackshaw and TomomiShimogori. Gene expression study in early postnatal mouse thalamus. 31st
Annual meeting of the Molecular Biology Society of Japan. Kobe, Japan (2008.
Dec).

7.

Tomomi Shimogori. Fgf8 controls regional identity in the developing thalamus.
The 31st Annual Meeting of the Japan Neuroscience Society, Tokyo, Japan(2008. Jul).

8.

Tomomi Shimogori and Ayane Kataoka. Fgf8 controls regional identity in thedeveloping thalamus. Gordon Conference, Neural Development, Nerport, RI,USA. (2008. Aug).

9.

Tomomi Shimogori and Ayane Kataoka. Fgf8 controls regional identity in thedeveloping thalamus. 17th Biennial Conference of the International Society for
Developmental Neuroscience, Asilomar, CA, USA. (2008. Jun).

10.

Tomomi Shimogori and Ayane Kataoka. Fgf8 controls regional identity in thedeveloping thalamus. IBRO sattelitte meeting, Cairns, Australia (2007. Jul).

11.

Tomomi Shimogori and Ayane Kataoka. Fgf8 controls regional identity in thedeveloping thalamus. IBRO 2007 World Congress, Melborne, Australia (2007.
Jul).

12.

Tomomi Shimogori and Ayane Kataoka. Developmental mechanism of
mammalian diencephalon. 16th Biennial Conference of the International Society
for Developmental Neuroscience, Banff, Alberta, Canada. (2006. Aug).

13.

Tomomi Shimogori. Japanese-American Frotiers of Science. Kanagawa, Japan.
(2005. Dec).
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