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In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9


Probing gene function in the mammalian brain can be greatly assisted with methods to manipulate the genome of neurons in vivo. The clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated endonuclease (Cas)9 from Streptococcus pyogenes (SpCas9)1 can be used to edit single or multiple genes in replicating eukaryotic cells, resulting in frame-shifting insertion/deletion (indel) mutations and subsequent protein depletion. Here, we delivered SpCas9 and guide RNAs using adeno-associated viral (AAV) vectors to target single (Mecp2) as well as multiple genes (Dnmt1, Dnmt3a and Dnmt3b) in the adult mouse brain in vivo. We characterized the effects of genome modifications in postmitotic neurons using biochemical, genetic, electrophysiological and behavioral readouts. Our results demonstrate that AAV-mediated SpCas9 genome editing can enable reverse genetic studies of gene function in the brain.

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Figure 1: Targeting of Mecp2 locus in the adult mouse brain with SpCas9.
Figure 2: Analysis of gene expression in SpCas9-mediated MeCP2 knockdown neurons.
Figure 3: Changes in response properties of visual cortex neurons after SpCas9-mediated MeCP2 knockdown.
Figure 4: Simultaneous, multiplex gene editing in the mouse brain.

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We thank A. Trevino and C. Le for technical assistance and the entire Zhang lab for technical support and critical discussions; we thank R. Platt (Broad Institute) and H. Worman (Columbia University) for sharing plasmids, R. Rikhye for providing a template for electrophysiology analysis; and X. Yu for statistical discussions. L.S. is a European Molecular Biology Organization (EMBO) Fellow and is supported by the Foundation for Polish Science. M.H. is supported by the Human Frontiers Scientific Program. A.B. holds a postdoctoral fellowship from the Simons Center for the Social Brain. N.H. is an EMBO Fellow and Y.L. is supported by Friends of the McGovern Institute Fellowship. M.S. is supported by grants from the US National Institutes of Health (NIH) (R01EY007023 and R01MH085802) and the Simons Foundation. F.Z. is supported by the National Institute of Mental Health (NIMH) through NIH Director's Pioneer Award (5DP1-MH100706), the NINDS through a NIH Transformative R01 grant (5R01-NS073124), the Keck, Merkin, Vallee, Damon Runyon, Searle Scholars, Klarman Family Foundation, Klingenstein, Poitras and Simons Foundations, and Bob Metcalfe. The authors plan on making the reagents widely available to the academic community through Addgene and to provide software tools via the Zhang lab website (

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Authors and Affiliations



L.S., M.H. and F.Z. developed the concept and designed experiments. L.S. and M.H. carried out CRISPR-Cas9-related experiments and analyzed data. A.B. designed and performed electrophysiological experiments and analyzed data. N.H., Y.L. and J.T. carried-out RNA sequencing experiments and analyzed data. Y.L. analyzed NGS data. L.S., M.H. and F.Z. wrote the manuscript with input from all authors.

Corresponding author

Correspondence to Feng Zhang.

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Competing interests

F.Z. is a scientific advisor of Editas Medicine and Horizon Discovery. A patent application has been filed relating to this work.

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Supplementary Figures 1–12 and Supplementary Tables 1–3 (PDF 1449 kb)

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Swiech, L., Heidenreich, M., Banerjee, A. et al. In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9. Nat Biotechnol 33, 102–106 (2015).

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