Engineering of the epigenome: synthetic biology to define functional causality and develop innovative therapies

The quickly evolving field of genome engineering has now also embraced epigenomics and promises to revolutionize the possibilities to functionally investigate and validate the importance of epigenetic modifications at any locus in the genome. These approaches will allow for the first time to determine if epigenetic changes are causal to observed phenotypic changes and will substantially further our understanding of the multifaceted roles of epigenetic modifications and their combinations in chromatin, which is key to the answer of many biomedical questions. Epigenome editing will help identify and evaluate the role of intergenic gene regulatory elements such as enhancers in the regulation of endogenous gene expression in a cell-type-specific context through targeted alteration of the local chromatin structure. Furthermore, and perhaps most exiting, editing of the epigenome has also the potential to provide in the near future new tools to correct disease-specific epigenetic modifications in a personalized manner by re-establishing normal gene expression programs in the targeted cells. Three major technological approaches have been pursued in the past to localize effector domains of epigenetic modifiers to a specific genomic context. They all can permanently alter the epigenetic code of the target region by depositing or removing specific epigenetic marks close to their binding site and thereby provide evidence for the role of an epigenetic mark at a locus of interest. These include transcription activator-like effectors (TALEs), zinc finger-based artificial transcription factors (ATFs) and the CRISPR/Cas9 system [1–4]. They all can be combined with a large number of effector domains, catalytically active protein fragments of epigenetic enzymes such as DNA methyltransferases, TETs and histone (de)methylases, acetyltransferases and deacetylases as well as transcriptional repressors and activators that are able to recruit chromatin modifying and remodeling complexes [4]. Initial studies using epigenome engineering tools have focused on the selective modulation of DNA methylation at specific loci using rationally designed zinc finger arrays. The clinically used DNA demethylating drugs are considered relatively safe because nonmalignant cells recover their ‘normal’ DNA methylation profile relatively rapidly. Nonetheless, they demethylate the entire genome of all cells regardless of the disease status of the cell. Therefore, strategies have been developed to target, for example, DNA demethylases such as the TET enzymes to hypermethylated promoters that are solely present in cancer cells and reactivate the corresponding gene that could have tumor suppressive properties using either zinc fingers [5] or TALEs [6]. On the other hand, genes specifically overexpressed in malignant cells can – to variable degrees – be silenced by targeting zinc finger-conjugated subunits of DNA Engineering of the epigenome: synthetic biology to define functional causality and develop innovative therapies