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Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex


Activity-dependent transcriptional responses shape cortical function. However, a comprehensive understanding of the diversity of these responses across the full range of cortical cell types, and how these changes contribute to neuronal plasticity and disease, is lacking. To investigate the breadth of transcriptional changes that occur across cell types in the mouse visual cortex after exposure to light, we applied high-throughput single-cell RNA sequencing. We identified significant and divergent transcriptional responses to stimulation in each of the 30 cell types characterized, thus revealing 611 stimulus-responsive genes. Excitatory pyramidal neurons exhibited inter- and intralaminar heterogeneity in the induction of stimulus-responsive genes. Non-neuronal cells showed clear transcriptional responses that may regulate experience-dependent changes in neurovascular coupling and myelination. Together, these results reveal the dynamic landscape of the stimulus-dependent transcriptional changes occurring across cell types in the visual cortex; these changes are probably critical for cortical function and may be sites of deregulation in developmental brain disorders.

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Change history

  • 11 May 2018

    In the version of this article initially published, the x-axis labels in Fig. 3c read Vglut, Gad1/2, Aldh1l1 and Pecam1; they should have read Vglut+, Gad1/2+, Aldh1l1+ and Pecam1+. In Fig. 4, the range values were missing from the color scales; they are, from left to right, 4–15, 0–15, 4–15 and 0–15 in Fig. 4a and 4–15, 4–15 and 4–8 in Fig. 4h. In the third paragraph of the main text, the phrase reading “Previous approaches have analyzed a limited number of inhibitory cell types, thus masking the full diversity of excitatory populations” should have read “Previous approaches have analyzed a limited number of inhibitory cell types and masked the full diversity of excitatory populations.” In the second paragraph of Results section “Diversity of experience-regulated ERGs,” the phrase reading “thus suggesting considerable divergence within the gene expression program responding to early stimuli” should have read “thus suggesting considerable divergence within the early stimulus-responsive gene expression program.” In the fourth paragraph of Results section “Excitatory neuronal LRGs,” the sentence reading “The anatomical organization of these cell types into sublayers, coupled with divergent transcriptional responses to a sensory stimulus, suggested previously unappreciated functional subdivisions located within the laminae of the mouse visual cortex and resembling the cytoarchitecture in higher mammals” should have read “The anatomical organization of these cell types into sublayers, coupled with divergent transcriptional responses to a sensory stimulus, suggests previously unappreciated functional subdivisions located within the laminae of the mouse visual cortex, resembling the cytoarchitecture in higher mammals.” In the last sentence of the Results, “sensory-responsive genes” should have read “sensory-stimulus-responsive genes.” The errors have been corrected in the HTML and PDF versions of the article.


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We thank E. Griffith and J. Gray for critical reading of the manuscript; the HMS Single Cell Core for sample processing; and D. Harmin, A. Veres, D. Kotliar, H. Finucane, Y. Reshef, B. Hall, T. Otis, and D. Malhotra for discussions. This work was supported by funding from National Institutes of Health (NIH) grant R01 NS028829 and the ROADS Program funded by F. Hoffmann-La Roche Ltd. to M.E.G.; NIH grant R01 NS046579 to B.L.S.; the William F. Milton Fund to D.R.H.; NIH grant T32GM007753 to M.A.N.; NIH Training Grant in the Molecular Biology of Neurodegeneration 5T32AG000222-23 to S.H.; and a Burroughs Wellcome Fund Career award at the scientific interface, an Edward J. Mallinckrodt Scholarship, and NCI grant R33CA212697 to A.M.K.

Author information

S.H., D.R.H., and M.A.N. conceived the study and designed all experiments. S.H. and D.R.H. developed the optimized dissociation protocol. S.H. and D.R.H. performed single-cell experiments with assistance from R.Z., A.M.K., and A.R. M.A.N. processed all sequencing data. S.H., M.A.N., and D.R.H. analyzed data with assistance from R.B.-M. and A.M.K. D.R.H., K.R., and L.C. carried out FISH experiments and imaging, D.R.H. analyzed the FISH data. M.C. and D.R.H. developed automated software for FISH analysis. S.H., D.R.H., M.A.N., and M.E.G. wrote the manuscript. M.E.G. and B.L.S. advised on all aspects of the study.

Competing interests

The authors declare no competing financial interests.

Correspondence to Bernardo L. Sabatini or Michael E. Greenberg.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1–24

  2. Life Sciences Reporting Summary

  3. Supplementary Table 1

    GEO terms for genes induced by drug-cocktail treatment

  4. Supplementary Table 2

    Cell-type enriched genes

  5. Supplementary Table 3

    The 611 induced genes across cell types and time points

  6. Supplementary Table 4

    GEO terms for sensory-experience-regulated genes

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Further reading

Fig. 1: Workflow and identification of cell types.
Fig. 2: Identification of sensory-stimulus-regulated genes.
Fig. 3: Diversity of experience-regulated ERGs.
Fig. 4: Sensory-experience-induced transcriptional responses in V1 excitatory neurons.
Fig. 5: Inhibitory neuronal LRGs.
Fig. 6: Light-induced transcriptional changes in non-neuronal cells.