Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Specific synapses develop preferentially among sister excitatory neurons in the neocortex


Neurons in the mammalian neocortex are organized into functional columns1,2. Within a column, highly specific synaptic connections are formed to ensure that similar physiological properties are shared by neuron ensembles spanning from the pia to the white matter. Recent studies indicate that synaptic connectivity in the neocortex is sparse and highly specific3,4,5,6,7,8 to allow even adjacent neurons to convey information independently9,10,11,12. How this fine-scale microcircuit is constructed to create a functional columnar architecture at the level of individual neurons largely remains a mystery. Here we investigate whether radial clones of excitatory neurons arising from the same mother cell in the developing neocortex serve as a substrate for the formation of this highly specific microcircuit. We labelled ontogenetic radial clones of excitatory neurons in the mouse neocortex by in utero intraventricular injection of enhanced green fluorescent protein (EGFP)-expressing retroviruses around the onset of the peak phase of neocortical neurogenesis. Multiple-electrode whole-cell recordings were performed to probe synapse formation among these EGFP-labelled sister excitatory neurons in radial clones and the adjacent non-siblings during postnatal stages. We found that radially aligned sister excitatory neurons have a propensity for developing unidirectional chemical synapses with each other rather than with neighbouring non-siblings. Moreover, these synaptic connections display the same interlaminar directional preference as those observed in the mature neocortex. These results indicate that specific microcircuits develop preferentially within ontogenetic radial clones of excitatory neurons in the developing neocortex and contribute to the emergence of functional columnar microarchitectures in the mature neocortex.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Morphological development of ontogenetic radial clones of excitatory neurons in the neocortex.
Figure 2: Synapse formation between sister excitatory neurons in ontogenetic radial clones.
Figure 3: A strong preference for synapse formation between sister excitatory neurons in ontogenetic radial clones.
Figure 4: A highly specific microcircuit forms among sister excitatory neurons in ontogenetic radial clones.


  1. Hubel, D. H. & Wiesel, T. N. Receptive fields, binocular interaction and functional architecture in the cat's visual cortex. J. Physiol. (Lond.) 160, 106–154 (1962)

    Article  CAS  Google Scholar 

  2. Mountcastle, V. B., Davies, P. W. & Berman, A. L. Response properties of neurons of cat’s somatic sensory cortex to peripheral stimuli. J. Neurophysiol. 20, 374–407 (1957)

    Article  CAS  Google Scholar 

  3. Kozloski, J., Hamzei-Sichani, F. & Yuste, R. Stereotyped position of local synaptic targets in neocortex. Science 293, 868–872 (2001)

    Article  CAS  Google Scholar 

  4. Markram, H., Lubke, J., Frotscher, M., Roth, A. & Sakmann, B. Physiology and anatomy of synaptic connections between thick tufted pyramidal neurones in the developing rat neocortex. J. Physiol. (Lond.) 500, 409–440 (1997)

    Article  CAS  Google Scholar 

  5. Song, S., Sjostrom, P. J., Reigl, M., Nelson, S. & Chklovskii, D. B. Highly nonrandom features of synaptic connectivity in local cortical circuits. PLoS Biol. 3, e68 (2005)

    Article  Google Scholar 

  6. Thomson, A. M., West, D. C., Wang, Y. & Bannister, A. P. Synaptic connections and small circuits involving excitatory and inhibitory neurons in layers 2–5 of adult rat and cat neocortex: triple intracellular recordings and biocytin labelling in vitro . Cereb. Cortex 12, 936–953 (2002)

    Article  Google Scholar 

  7. Yoshimura, Y., Dantzker, J. L. & Callaway, E. M. Excitatory cortical neurons form fine-scale functional networks. Nature 433, 868–873 (2005)

    Article  ADS  CAS  Google Scholar 

  8. Yoshimura, Y. & Callaway, E. M. Fine-scale specificity of cortical networks depends on inhibitory cell type and connectivity. Nature Neurosci. 8, 1552–1559 (2005)

    Article  CAS  Google Scholar 

  9. Ohki, K. et al. Highly ordered arrangement of single neurons in orientation pinwheels. Nature 442, 925–928 (2006)

    Article  ADS  CAS  Google Scholar 

  10. Ohki, K., Chung, S., Ch'ng, Y. H., Kara, P. & Reid, R. C. Functional imaging with cellular resolution reveals precise micro-architecture in visual cortex. Nature 433, 597–603 (2005)

    Article  ADS  CAS  Google Scholar 

  11. Sato, T. R., Gray, N. W., Mainen, Z. F. & Svoboda, K. The functional microarchitecture of the mouse barrel cortex. PLoS Biol. 5, e189 (2007)

    Article  Google Scholar 

  12. Maldonado, P. E., Godecke, I., Gray, C. M. & Bonhoeffer, T. Orientation selectivity in pinwheel centers in cat striate cortex. Science 276, 1551–1555 (1997)

    Article  CAS  Google Scholar 

  13. Noctor, S. C., Flint, A. C., Weissman, T. A., Dammerman, R. S. & Kriegstein, A. R. Neurons derived from radial glial cells establish radial units in neocortex. Nature 409, 714–720 (2001)

    Article  ADS  CAS  Google Scholar 

  14. Noctor, S. C., Martinez-Cerdeno, V., Ivic, L. & Kriegstein, A. R. Cortical neurons arise in symmetric and asymmetric division zones and migrate through specific phases. Nature Neurosci. 7, 136–144 (2004)

    Article  CAS  Google Scholar 

  15. Miyata, T., Kawaguchi, A., Okano, H. & Ogawa, M. Asymmetric inheritance of radial glial fibers by cortical neurons. Neuron 31, 727–741 (2001)

    Article  CAS  Google Scholar 

  16. Malatesta, P., Hartfuss, E. & Gotz, M. Isolation of radial glial cells by fluorescent-activated cell sorting reveals a neuronal lineage. Development 127, 5253–5263 (2000)

    CAS  Google Scholar 

  17. Tamamaki, N., Nakamura, K., Okamoto, K. & Kaneko, T. Radial glia is a progenitor of neocortical neurons in the developing cerebral cortex. Neurosci. Res. 41, 51–60 (2001)

    Article  CAS  Google Scholar 

  18. Rakic, P. Mode of cell migration to the superficial layers of fetal monkey neocortex. J. Comp. Neurol. 145, 61–83 (1972)

    Article  CAS  Google Scholar 

  19. Rakic, P. Specification of cerebral cortical areas. Science 241, 170–176 (1988)

    Article  ADS  CAS  Google Scholar 

  20. Kornack, D. R. & Rakic, P. Radial and horizontal deployment of clonally related cells in the primate neocortex: relationship to distinct mitotic lineages. Neuron 15, 311–321 (1995)

    Article  CAS  Google Scholar 

  21. Cepko, C. L. et al. Studies of cortical development using retrovirus vectors. Cold Spring Harb. Symp. Quant. Biol. 55, 265–278 (1990)

    Article  CAS  Google Scholar 

  22. Walsh, C. & Cepko, C. L. Clonally related cortical cells show several migration patterns. Science 241, 1342–1345 (1988)

    Article  ADS  CAS  Google Scholar 

  23. Walsh, C. & Cepko, C. L. Clonal dispersion in proliferative layers of developing cerebral cortex. Nature 362, 632–635 (1993)

    Article  ADS  CAS  Google Scholar 

  24. Hensch, T. K. Critical period plasticity in local cortical circuits. Nature Rev. Neurosci. 6, 877–888 (2005)

    Article  CAS  Google Scholar 

  25. Micheva, K. D. & Beaulieu, C. Quantitative aspects of synaptogenesis in the rat barrel field cortex with special reference to GABA circuitry. J. Comp. Neurol. 373, 340–354 (1996)

    Article  CAS  Google Scholar 

  26. Stern, E. A., Maravall, M. & Svoboda, K. Rapid development and plasticity of layer 2/3 maps in rat barrel cortex in vivo . Neuron 31, 305–315 (2001)

    Article  CAS  Google Scholar 

  27. Sjostrom, P. J., Turrigiano, G. G. & Nelson, S. B. Rate, timing, and cooperativity jointly determine cortical synaptic plasticity. Neuron 32, 1149–1164 (2001)

    Article  CAS  Google Scholar 

  28. Thomson, A. M. & Bannister, A. P. Interlaminar connections in the neocortex. Cereb. Cortex 13, 5–14 (2003)

    Article  Google Scholar 

  29. Douglas, R. J. & Martin, K. A. Neuronal circuits of the neocortex. Annu. Rev. Neurosci. 27, 419–451 (2004)

    Article  CAS  Google Scholar 

  30. Kriegstein, A., Noctor, S. & Martinez-Cerdeno, V. Patterns of neural stem and progenitor cell division may underlie evolutionary cortical expansion. Nature Rev. Neurosci. 7, 883–890 (2006)

    Article  CAS  Google Scholar 

Download references


We thank A. L. Joyner, J. Kaltschmidt, Y. Hayashi and Y. Chin for comments on the manuscript; and S. C. Noctor and F. H. Gage for providing the 293gp NIT–GFP retrovirus packaging cell line; and the Shi laboratory members for insightful discussion. We are grateful for support from the March of Dimes Foundation, the Whitehall Foundation, the Klingenstein Foundation, the DANA Foundation, the Autism Speaks Foundation, the National Alliance for Research on Schizophrenia and Depression (NARSAD) and the National Institutes of Health (to S.-H.S.).

Author Contributions Y.-C.Y. and S.-H.S. conceived the experiments. Y.-C.Y. conducted the electrophysiology and imaging experiments. R.S.B and X.W. helped with in utero virus injection. Y.-C.Y. and S.-H.S. analysed the data and wrote the manuscript.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Song-Hai Shi.

Supplementary information

Supplementary Figures

This file contains Supplementary Figures 1-5 with Legends (PDF 1812 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Yu, YC., Bultje, R., Wang, X. et al. Specific synapses develop preferentially among sister excitatory neurons in the neocortex. Nature 458, 501–504 (2009).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing