Synthetic Biology

Many chromatin regulatory proteins or "reader proteins" contain single or multiple chromatin reader domains that bind to specific modifications. The combinatorial readout of multiple histone marks and nucleosome features by reader proteins enhances their binding and increases their residence time on chromatin. More importantly, it possibly contributes to context-dependent targeting of regulatory proteins to particular sites on the genome by reading multiple marks at the same time.

Can we engineer reader proteins with novel properties that allow us to target specific portions of the genome? Yes, we can!

Recently, we used parts of proteins, so-called “reader domains”, that interact with particular DNA or histone modifications. These reader domains are present in many regulatory proteins and are required for their site-specific localization to the genome. As a proof of concept, we first used natural reader domains of well-studied chromatin-interacting proteins as modular building blocks to develop so-called “engineered chromatin readers” (eCRs). By stably expressing eCRs in mouse embryonic stem cells and measuring their subnuclear localization, genomic distribution, and histone–modification–binding preference, we could demonstrate their selectivity for chromatin modifications and the suitability of eCRs to study chromatin readout in living cells.

Notably, we found a simple design principle (multivalency) to yield selective histone-mark readers, which has also been shown by other studies (Mauser et al., 2017; Delachat et al., 2018; Tekel et al., 2018). The modular architecture of eCRs allows us to take virtually any reader domain found in nature and build eCRs that are selective for combinatorial marks. Our strategy allowed us to develop powerful probes for genome-wide binding analysis and live-cell imaging. We are excited to use eCRs soon to study other histone marks and combinatorial modifications.