Tata Institute of Fundamental Research


Shubha Tole


Genetic mechanisms and signaling pathways in the developing brain


Cerebral cortex and the amygdala are the two most complex brain structures. The cortex is responsible for higher brain functions- perception, language, learning, memory; the amygdala is the "emotion center" of the brain. The broad interests of our group are in the genetic and epigenetic mechanisms that control the formation of these highly specialized structures. We use "knockout" and transgenic approaches, in-utero and tissue culture perturbation techniques, ChIP-seq and Mass spectrometry, neurocircuitry tracing and CLARITY-based approaches, and behavioral paradigms to pursue these questions.


Selected Publications


Pal S, Dwivedi D, Pramanik T, Godbole G, Iwasato T, Jabaudon D, Bhalla US and Tole S, (2021) An early cortical progenitor-specific mechanism regulates thalamocortical innervation.   Journal of Neuroscience41(32), 6822

*Kinare V, *Iyer A, Padmanabhan H, Godbole G, Khan T, Khatri Z, Maheshwari U, Bhavana M, Tole S (2020) An evolutionarily conserved Lhx2-Ldb1 interaction regulates the  acquisition of hippocampal cell fate and regional identity.  Development147(20)

Godbole G, Shetty AS, Roy A, D’souza L, Chen B, Miyoshi G, Fishell G, #Tole S (2018) Hierarchical genetic interactions between FOXG1 and LHX2 regulate the formation of the cortical hem in the developing telencephalon.  Development145(1)

Bhavana M, Keruzore M, Roy B, Pradhan S, Shetty AS, Kinare V, D’Souza L, Maheshwari U, Karmodiya K, Suresh A, Galande S, #Bellefroid E, and #Tole S (2017b)  Dmrt5, a novel neurogenic factor, reciprocally regulates Lhx2 to control the neuron-glia cell fate switch in the developing hippocampus  Journal of Neuroscience 37(46):11245

Bhavana M, Khatri Z, Maheshwari U, Gupta R, , Roy B, Pradhan S, Karmodiya K, Padmanabhan H, Shetty AS, Balaji CH, Kolthur U, Macklis JD, Galande S, and #Tole S (2017).   Lhx2 interacts with the NURD complex and epigenetically modulates cortical neuron subtype regulators Fezf2 and Sox11   Journal of Neuroscience 2836-16.  PMID: 27909100

 Shetty AS,  Godbole G, Maheshawari U, Padmanabhan H, Chaudhary R, Muralidharan B, Hou P-S, Monuki ES, Kuo H-C, V Rema, #Tole S (2013) Lhx2 regulates a cortex-specific mechanism for barrel formation    PNAS  doi:10.1073/pnas.1311158110

 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 mammalian accessory olfactory bulb revealed by an evolutionarily conserved migratory stream    Nature Neuroscience 16(2):157-65

Subramanian L, Sarkar A, Ashwin S, Muralidharan B, Hari P, Piper M, Monuki ES, Bach I,Gronostajski R, Richards R, and #Tole, S (2011)Transcription factor Lhx2is necessary and sufficient to suppress astrogliogenesis and promote neurogenesis in the developing hippocampus. PNAS108(27) E265- E274

 Mangale VS, Hirokawa KE, Satyaki PRV, GokulchandranN, ChikbireS, Subramanian L, Shetty AS, Martynoga B, Paul J, Mai MV, Li Y, Flanagan LA, Tole S#, and Monuki ES #  (2008)  Lhx2 selector activity specifies cortical identity  and suppresses hippocampal organizer fate  Science,319:304-309 # corresponding author

“Perspectives” based on this paper:  E. A. Grove “Organizing the Source of Memory” Science (319)  288-289

A highlight based on this paper:  M. H. Flight “Instructions for the Hippocampus”  Nature Reviews Neuroscience 9 (3): 164-165                        

Remedios, R., Huilgol, D., Saha, B., Hari, P., Bhatnagar, L., Kowalczyk T., Hevner R. F., Suda Y., Aizawa S.,  Ohshima, T., Stoykova, A., Tole, S#. (2007)  A novel stream of amygdaloid cells from the caudal telencephalon reveals a developmental link between the amygdala and the neocortex    Nature Neuroscience 10 (9): 1141–1150

 “News and Views” based on this paper:  J. M. Deussing and W. Wurst “Amygdala and   Neocortex:       Common Origins and Shared Mechanisms”    Nature Neuroscience 10 (9):  1081-1082



Tole S. and Vale, R.  (2010).  Young leaders for Biology in India.  Science 329: 1441.  (Editorial)

Book Chapter:

Tole S. and Hebert J.  Telencephalon Patterning. “Cellular Migration and Formation of Neuronal Connections:  Comprehensive Developmental Neuroscience” (2013) John Rubenstein and PaskoRakic (Eds).  Academic Press.  ISBN: 978-0-12-397265-1

Meeting Report:  

Tole S. and Shashidhara LS (2018) Gender-sensitization in Indian science: attitudes and action items” Tole and Shashidhara, 2018, in press, Current Science

Personal story:  

Nature Cell Biology’s  “Turning Points” series: Mentorship comes from many sources.

Tole, Nature Cell Biology 20:1010 (2018)

Blogs:  https://indiabioscience.org/authors/ShubhaTole

                Taking the “ME” out of Mentorship 

                Scientist and Mommy  

                How to choose which institution or which lab to join?

                One possible plug for the leaky pipeline 

                Are we doing enough?

                How are we viewing collaborations? 

                Advice for students starting out in research

Advice for students starting out in research


  • Room B-304
  • Tel: +91 22 2278 2878
  • shubhatole @ gmail.com
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