Neuroepigenetic Editing

Abstract

Epigenetic regulation is intrinsic to basic neurobiological function as well as neurological disease. Regulation of chromatin-modifying enzymes in the brain is critical during both development and adulthood and in response to external stimuli. Biochemical studies are complemented by numerous next-generation sequencing (NGS) studies that quantify global changes in gene expression, chromatin accessibility, histone and DNA modifications in neurons and glial cells. Neuroepigenetic editing tools are essential to distinguish between the mere presence and functional relevance of histone and DNA modifications to gene transcription in the brain and animal behavior. This review discusses current advances in neuroepigenetic editing, highlighting methodological considerations pertinent to neuroscience, such as delivery methods and the spatiotemporal specificity of editing and it demonstrates the enormous potential of epigenetic editing for basic neurobiological research and therapeutic application.

Keywords: Epigenetic editing; chromatin; neuroscience; psychiatric disease.

Fig. 1

Epigenetic editing tools. Three main approaches to epigenetic editing have been applied in neurons. ZFPs and TALEs rely on a protein DNA-binding domain tethered to an effector domain, while the CRISPR/dCas9 system utilizes an RNA–DNA interaction to guide the dCas9-effector domain fusion to the target gene. Effector domains act to modify histone tails and/or DNA at target loci. ZFPs are shown with Zn²⁺ stabilizing ion (grey dot) and TALEs are shown with C- and N-terminal domains in yellow

Fig. 2

Brain delivery methods. (a–c) The majority of published neuroepigenetic editing studies rely on virally mediated expression of editing tool in brain. Several viral vectors are available, including HSV [31, 72, 73], AAV [29, 53, 56, 83, 100, 124], and LV [64, 75, 77, 78, 125]. HSV has emerged as the most widely applied in vivo delivery method, due to its large packaging size, neuronal specificity, and relative safety due to the lack of genomic integration. (d, e) Recent methods for nonviral delivery of purified epigenetic editing constructs. (d) Purified dCas9/sgRNA ribonucleoprotein is modified with an affinity array of nuclear localization signals to allow cell penetrance [79, 80]. In (e), a purified protein consisting of a ZFP fused to a cell-penetrating peptide gains entry to neurons [81]

Fig. 3

Spatial and temporal control of epigenetic editing. (a) Cell-type specific expression of an epigenetic editing tool by injecting Cre-dependent virus into the brain of a transgenic animal expressing Cre recombinase in specific cell types [73]. (b) Light-inducible dimerization of dCas9 with a functional domain is accomplished by fusion of each to CRY2 and C1BN domains, respectively. Upon blue-light stimulation, CRY2 and C1BN heterodimerize, bringing the effector domain in proximity with the dCas9-bound locus [51]. (c) Chemically-inducible CRISPR-mediated epigenetic editing is accomplished by expression of a split-dCas9 N- and C-terminals fused to rapamycin-sensitive heterodimerization domains, FRB and FKBP, respectively. Upon rapamycin administration, dCas9 halves are brought into proximity and translocate to the nucleus [75]