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In vivo locus-specific editing of the neuroepigenome

Nature Reviews Neuroscience volume 21, pages 471–484 (2020)Cite this article

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Abstract

Studies over the past several decades have identified numerous epigenetic mechanisms associated with pathological states in psychiatric and neurological disease. Until recently, studies investigating chromatin-regulatory proteins, using overexpression or knockdown approaches, did not establish causal roles for epigenetic modifications at specific genes because these techniques typically affect hundreds or thousands of genomic loci. In this Review, we describe recent efforts in using locus-specific neuroepigenome editing in vivo to, for the first time, define causal relationships between a single chromatin modification at a specific gene in a defined cell population and downstream measures at the molecular, cellular, circuit and behavioural levels. We briefly introduce three epigenome-editing platforms: zinc-finger proteins, transcriptional activator-like effectors and clustered regularly interspaced short palindromic repeats (CRISPR). We then explore the development of in vivo neuroepigenome-editing tools and their applications to resolve epigenetic contributions to the pathophysiology of brain diseases. We also discuss technical considerations for in vivo neuroepigenome-editing experiments and ongoing innovations in the field, including new tools to investigate chromatin marks, manipulate chromatin topology and induce epigenetic modifications at multiple genes in the same cell. Lastly, we explore the potential clinical applications of in vivo neuroepigenome editing for treating brain pathology.

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Fig. 1: In vivo neuroepigenome-editing tools.
Fig. 2: Overview of CRISPRa/CRISPRi techniques.
Fig. 3: CRISPR-based neuroepigenome-editing tools.
Fig. 4: Innovative neuroepigenome-editing tools.

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Acknowledgements

The authors are very grateful to J. K. Gregory for her help with the figures in this Review.

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Author notes

  1. These authors contributed equally: Yun Young Yim, Collin D. Teague.

Authors and Affiliations

  1. Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA

    Yun Young Yim, Collin D. Teague & Eric J. Nestler

  2. Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA

    Yun Young Yim, Collin D. Teague & Eric J. Nestler

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  1. Yun Young Yim
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E.J.N. made substantial contributions to the discussion and editing of the content. Y.YY. and C.D.T. wrote the article. All authors reviewed and edited the article before submission.

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Correspondence to Eric J. Nestler.

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Nature Reviews Neuroscience thanks J. Day, H. Yang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Glossary

Transcription activator-like effector

(TALE). DNA-binding protein derived from bacteria (Xanthomonas) that regulates gene expression.

Clustered regularly interspaced short palindromic repeats

(CRISPR). A component of the adaptive immune system in bacteria and archaea that cleaves foreign nucleic acid sequences. It is used routinely in the laboratory to enable targeted genetic and epigenetic manipulations.

Guide RNA

(gRNA). A synthetic RNA that guides clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) to a specific DNA sequence in the genome.

VP64

A complex of four copies of VP16 (a viral protein sequence of 16 amino acids) that activates gene transcription.

Zinc-finger proteins

(ZFPs). Proteins consisting of zinc ion-regulated Cys2-His2 domains that recognize specific 18-bp sequences of DNA. These proteins can be fused to various effector proteins, including nucleases and chromatin-modifying proteins.

Transcription factor

(TF). Protein that binds to specific sequences of DNA and regulates gene expression through the recruitment of chromatin-modifying enzymes and other proteins.

Fosb

An immediate early gene that encodes full-length FOSB and a truncated splice variant ∆FOSB, and that has served as a useful target for the development of novel neuroepigenome-editing tools.

cAMP response element-binding protein

(CREB). A ubiquitously expressed transcription factor implicated in diverse functions in the central nervous system and periphery.

Protospacer adjacent motif

(PAM). A short DNA sequence upstream of the target gene that is recognized by clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9).

CRISPR activation

(CRISPRa). A clustered regularly interspaced short palindromic repeats (CRISPR) system that uses potent activation domains, such as the viral transcription factor VP64, to increase gene expression.

CRISPR interference

(CRISPRi). A clustered regularly interspaced short palindromic repeats (CRISPR) system that uses repressive domains, such as the Krüppel-associated box (KRAB) domain, to suppress gene expression.

SunTag

A clustered regularly interspaced short palindromic repeats (CRISPR)-based method that uses a repeating peptide array to recruit multiple copies of single-chain variable fragment (scFv)-fused effector proteins to a target gene.

ZFP189

A putative transcription factor whose gene is a target of cAMP response element-binding protein (CREB). Recent studies suggest that this protein is involved in regulating synaptic plasticity and behavioural responses to stress.

DNMT3A

Enzyme that catalyses the addition of methyl groups to DNA.

Chromatin loop reorganization using CRISPR–dCas9

(CLOuD9). A clustered regularly interspaced short palindromic repeats (CRISPR) system that uses chemically induced ligation to selectively and reversibly establish chromatin loops.

CRISPR genome organization

(CRISPR-GO). A clustered regularly interspaced short palindromic repeats (CRISPR) system that uses chemically induced ligation to bring loci in close proximity to nuclear subcompartments.

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Yim, Y.Y., Teague, C.D. & Nestler, E.J. In vivo locus-specific editing of the neuroepigenome. Nat Rev Neurosci 21, 471–484 (2020). https://doi.org/10.1038/s41583-020-0334-y

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