Epigenome Editing: State of the Art, Concepts, and Perspectives

Numerous studies have demonstrated that targeted deposition or removal of chromatin modifications (epigenome editing) is a powerful approach for functional studies of locus-specific chromatin modifications and their relation to gene expression and other processes. Epigenome editing holds great potential as a therapeutic approach in the clinic for durable regulation of disease-related genes and in cellular reprogramming. Before the full potential of epigenome editing can be realized, numerous questions related to the function, regulatory logic, and maintenance of chromatin modifications need to be answered. The question of specificity of the DNA recognition domain needs to be addressed in a case-by-case manner. The activity of the EpiEffector (catalytic domain of a chromatin-modifying enzyme) needs to be tuned to achieve optimal chromatin modulation. Epigenome editing refers to the directed alteration of chromatin marks at specific genomic loci by using targeted EpiEffectors which comprise designed DNA recognition domains (zinc finger, TAL effector, or modified CRISPR/Cas9 complex) and catalytic domains from a chromatin-modifying enzyme. Epigenome editing is a promising approach for durable gene regulation, with many applications in basic research including the investigation of the regulatory functions and logic of chromatin modifications and cellular reprogramming. From a clinical point of view, targeted regulation of disease-related genes offers novel therapeutic avenues for many diseases. We review here the progress made in this field and discuss open questions in epigenetic regulation and its stability, methods to increase the specificity of epigenome editing, and improved delivery methods for targeted EpiEffectors. Future work will reveal if the approach of epigenome editing fulfills its great promise in basic research and clinical applications. Epigenome editing refers to the directed alteration of chromatin marks at specific genomic loci by using targeted EpiEffectors which comprise designed DNA recognition domains (zinc finger, TAL effector, or modified CRISPR/Cas9 complex) and catalytic domains from a chromatin-modifying enzyme. Epigenome editing is a promising approach for durable gene regulation, with many applications in basic research including the investigation of the regulatory functions and logic of chromatin modifications and cellular reprogramming. From a clinical point of view, targeted regulation of disease-related genes offers novel therapeutic avenues for many diseases. We review here the progress made in this field and discuss open questions in epigenetic regulation and its stability, methods to increase the specificity of epigenome editing, and improved delivery methods for targeted EpiEffectors. Future work will reveal if the approach of epigenome editing fulfills its great promise in basic research and clinical applications. direct and targeted treatment of the major cause of a disease or phenotypic state. the process of converting one cell type into another by changing the gene expression program of the cell. the structural and functional interplay and coexistence of histone and DNA modifications within chromatin. nucleoprotein complex containing DNA, histones, non-histone proteins, and RNA. The basic structural unit of chromatin is the nucleosome, consisting of 147 bp of DNA wrapped around an octamer of histones H3, H4, H2A, and H2B. a prokaryotic immune system which protects bacterium against foreign DNA such as plasmids and phages. Mechanistically, in its simplest form, a nuclease (Cas9) binds to an appropriate small guide RNA molecule of the CRISPR class which targets the entire complex to its complementary target DNA sequence. oxidation of the 5-methylcytosine to 5-hydroxymethylcytosine and higher oxidation states. This process is the first step in DNA demethylation and the modified bases function as a chromatin modification. addition of a methyl group on the C5 position of cytosine residues in DNA, typically in a CpG context, by enzymes termed DNA methyltransferases. DNA adenine-N6 and DNA cytosine-N4 methylation is not discussed here. scientific field studying mitotically and/or meiotically heritable changes in gene function that do not rely on changes in DNA sequences. the sum of all chromatin modifications which may or may not be heritable (epigenetic). enzymatically introduced covalent modification of histone proteins, including lysine acetylation, lysine and arginine methylation, lysine ubiquitination, serine or threonine phosphorylation, among others. an epigenetic phenomenon where particular alleles are expressed in a parent-of-origin-dependent manner. a type of pluripotent stem cells that are generated by artificial cellular reprogramming of mature adult cells. a synthetic biology technique that uses light to control genetic circuits in living tissues. an interdisciplinary branch of biology concerned with the design of novel biological devices, biological systems, and biological machines. proteins secreted by Xanthomonas bacteria. They recognize target DNA sequences through a central repeat domain consisting of a variable number of ∼34 amino acid repeats showing a one-to-one correspondence between the identity of two hypervariable crucial amino acids (at the 12th and 13th positions) in each repeat and one DNA base in the target sequence. a protein domain with a finger-like protrusion that is characterized by coordination of zinc ion(s) to stabilize its fold. There is a colinearity between the protein sequence of the zinc finger and its target DNA sequence, with each finger mainly recognizing three base pairs.