Chromosomes are composed of genomic DNA and associated protein components that exert powerful regulatory effects. The 2 nm nucleosome represents the functional unit of chromatin, comprising 1.7 turns of genomic DNA (~ 147 bp) wrapping an octamer of histone proteins. Post-translational modification (PTM) of the histones (e.g. methylation, acetylation or ubiquitination) represents a central epigenetic regulatory mechanism, with specific modifications recruiting effector proteins. Effector proteins (or more often protein complexes) can include transcription factors responsible for initiating or blocking the expression of specific genes. The histone code hypothesis asserts that certain combinations of histone PTMs on a given nucleosome exert an ensemble impact on downstream gene expression through the recruitment of various effector proteins and complexes. Aberrant PTM regulation has been linked to changes in gene expression associated with specific disease states. Given the link between PTMs and disease, enzymes responsible for the addition and removal of certain PTMs have become the targets of drug discovery efforts with several compounds achieving marketing clearance. A broad range of compelling epigenetic drug targets therefore exist, including enzymes that add PTMs to histone proteins ('writers'), those that bind specific PTMs ('readers'), and those that remove PTMs ('erasers'). To study these interactions, peptides or recombinant histones can be synthetically modified to contain PTMs, but these substrates fail to replicate chromatin architecture. EpiCypher(tm) has pioneered the production of PTM-modified nucleosomes called designer nucleosomes. While these methods are effective, synthesis of a single new designer nucleosome can take 6-12 weeks, depending on the number of histone PTMs to add and the quality control steps required to ensure a ? 95% pure product. Condensing this process to 1 or 2 weeks would allow EpiCypher to produce a greater number of modified nucleosomes, dramatically expanding the utility of these reagents. Current screening of a given writer, reader or eraser for PTM-context dependent activities requires the use of either hundreds of modified peptides or a priori knowledge of the PTMs of interest to focus on a restricted handful of designer nucleosomes. Rapid, high-throughput manufacturing of PTM-carrying nucleosomes will enable EpiCypher to load each well of a 96-well plate with unique nucleosomes, enabling a dramatic increase in the throughput of these assays with substrates that more accurately represent in vivo chromatin structure. Recent research advancements have developed means to rapidly synthesize proteins carrying specific PTMs using AMBER suppression technology. Continuing these research efforts, we will develop, for the first time, methods for commercial-scale synthesis of designer nucleosomes carrying mono-, di- or trimethyl PTMs. This innovative advancement in designer nucleosome manufacturing will provide a transformational opportunity for drug discovery and the identification of novel therapeutic strategies.

Public Health Relevance

Post-translational modification (PTM) of histone proteins represents a central epigenetic regulatory mechanism, with specific modifications regulating the recruitment of effector proteins to chromatin, thereby potentiating or inhibiting downstream gene expression programs. To date, recombinant nucleosomes are slow to produce and modify, limiting their utility in high-throughput screening applications. Here, EpiCypher will optimize a novel means of scaling the production of PTM-modified nucleosomes, enabling the use of designer nucleosomes in high-throughput screens for novel drug discovery and innovative assay development.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Small Business Innovation Research Grants (SBIR) - Phase I (R43)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-IMST-J (15)B)
Program Officer
Preusch, Peter
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Epicypher, Inc.
Chapel Hill
United States
Zip Code