Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction

Abstract

DNA forms conformational states beyond the right-handed double helix; however, the functional relevance of these noncanonical structures in the brain remains unknown. Here we show that, in the prefrontal cortex of mice, the formation of one such structure, Z-DNA, is involved in the regulation of extinction memory. Z-DNA is formed during fear learning and reduced during extinction learning, which is mediated, in part, by a direct interaction between Z-DNA and the RNA-editing enzyme Adar1. Adar1 binds to Z-DNA during fear extinction learning, which leads to a reduction in Z-DNA at sites where Adar1 is recruited. Knockdown of Adar1 leads to an inability to modify a previously acquired fear memory and blocks activity-dependent changes in DNA structure and RNA state—effects that are fully rescued by the introduction of full-length Adar1. These findings suggest a new mechanism of learning-induced gene regulation that is dependent on proteins that recognize alternate DNA structure states, which are required for memory flexibility.

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Fig. 1: Adar1 binds to DNA and targets DNA repetitive elements in response to behavioral training.
Fig. 2: Adar1 knockdown impairs memory updating after extinction training.
Fig. 3: Z-DNA is a critical modulator of activity-dependent transcription.
Fig. 4: Adar1–Z-DNA interaction at the Nrxn3 locus modulates the expression of transcripts derived from a noncoding region enriched with SINEs.
Fig. 5: RNA editing enriched at SINEs and LINEs in activated neurons.
Fig. 6: Editing of RNA derived from SINEs and LINEs requires Adar1 binding to DNA.
Fig. 7: Fear extinction requires both Adar1 Z-DNA-binding and RNA-editing domains.

Data availability

All data and code used to generate the data are available upon reasonable request to the authors.

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Acknowledgements

The authors gratefully acknowledge grant support from the National Institutes of Health (R01MH105398-TWB) and the National Health and Medical Research Council (GNT1145172 and GNT1160823-TWB), the ARC (GNT190101078-XL), the Westpac Future Scholars program (E.L.Z., L.J.L. and S.U.M.) and postgraduate scholarships from the Natural Sciences and Engineering Research Council (P.R.M.) and the University of Queensland (P.R.M., E.L.Z., L.J.L., D.B., J.Y. and S.U.M.). We would also like to thank R. Tweedale for helpful editing of the manuscript.

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Authors

Contributions

P.R.M designed and performed all wet lab and behavioral experiments and wrote the manuscript with T.W.B. Q.Z. performed all the bioinformatics analysis. X.L. and W.W. assisted in experimental design and ChIP-seq experiments. A.P. assisted in the production of lentivirus. E.Z, L.J.L. and S.U.M. assisted with behavioral experiments. D.B. assisted with bioinformatic analysis. Z.W., J.Y. and W.S.L. assisted with western blots and qPCR. A.G. assisted in producing and validating the ADAR1 mutant constructs. C.W. contributed reagents and helped write the manuscript. T.W.B. conceived the study, designed experiments and wrote the manuscript.

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Correspondence to Timothy W. Bredy.

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The authors declare no competing interests.

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Peer review information Nature Neuroscience thanks Alan Herbert, Larry Zweifel and the other, anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Data from this paper can be accessed at PRJNA545193.

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Supplementary Figs. 1–9 and Supplementary Tables 1–3.

Reporting Summary

.Supplementary Table

Supplementary Table 1. Genome-wide ADAR1 significant peaks in Excel file.

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Source Data Fig. 1

Unprocessed western blots for Fig. 1

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Marshall, P.R., Zhao, Q., Li, X. et al. Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction. Nat Neurosci (2020). https://doi.org/10.1038/s41593-020-0627-5

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