Synthetic epigenetics-towards intelligent control of epigenetic states and cell identity

Abstract

Epigenetics is currently one of the hottest topics in basic and biomedical research. However, to date, most of the studies have been descriptive in nature, designed to investigate static distribution of various epigenetic modifications in cells. Even though tremendous amount of information has been collected, we are still far from the complete understanding of epigenetic processes, their dynamics or even their direct effects on local chromatin and we still do not comprehend whether these epigenetic states are the cause or the consequence of the transcriptional profile of the cell. In this review, we try to define the concept of synthetic epigenetics and outline the available genome targeting technologies, which are used for locus-specific editing of epigenetic signals. We report early success stories and the lessons we have learned from them, and provide a guide for their application. Finally, we discuss existing limitations of the available technologies and indicate possible areas for further development.

Keywords: CRISPR; Cell fate; Epigenetic editing; Epigenetics; Synthetic epigenetics; TALE; Targeted epigenome modification; Zinc fingers.

Figure 1

The concept of epigenetic editing. Targeting device, a sequence-specific DNA binding domain which can be redesigned to recognize desired sequences is fused to an effector domain, which can modify the epigenetic state of the targeted locus, leading to a persistent biological effect (gene activation or repression). Green lollipops represent introduced modification of either DNA bases or histone tails.

Figure 2

Structural models of possible epigenetic editing devices. The structural models of the proteins were taken from PDB repository (zinc finger [PDB:1P47], TALE [PDB:2YPF], CRISPR/Cas9 [PDB:4OO8], M.HhaI [PDB:5MHT], Dnmt3a/3L [PDB:2QRV], TET2 [PDB:4NM6], nucleosome [PDB:1AOI], a 21 amino acid linker was generated in PyMol, and 60 bp DNA sequence was generated with the make-na server (http://structure.usc.edu/make-na/server.html)). The models are drawn to scale and should provide an idea of the architecture of the synthetic constructs used for epigenetic editing. Modelling was done manually in PyMol. Zinc finger, DNA-bound zinc finger array fused to M.HhaI; TALE, synthetic TALE array fused to the catalytic domain of human TET2; CRISPR/Cas9, Cas9 protein fused to a Dnmt3a/Dnmt3L hetero-tetramer. The distances in base pairs and angstroms are indicated.