EpiCypher is an epigenetics company founded in 2012 by Drs. Mark Bedford, Or Gozani, Brian Strahl, and James Bone in response to the growing demand for high-quality reagents and tools to study chromatin regulation and enable epigenetics-focused drug development.

EpiCypher is the global leader in recombinant nucleosome manufacturing and development. Using proprietary methods, we are continuously adding to the world’s largest collection of highly pure modified recombinant “designer” nucleosomes (dNucs). EpiCypher’s broad dNuc diversity is providing a powerful tool to decipher the histone code and accelerate drug development. Shah et al., Wang et al., and Weinberg et al. (see below) are just a few examples of the many benefits of using nucleosome substrates for epigenetics studies.

EpiCypher leverages dNuc technology for a wide range of applications, including: SNAP-ChIP® Spike-in Controls (for antibody profiling and quantitative ChIP), EpiDyne® substrates (for characterizing chromatin remodeling enzyme complexes and inhibitors), and dCypher™ assays (for interrogation of epigenetic protein-histone PTM binding interactions). We also offer a suite of high-quality recombinant histone binding proteins, enzymes, peptides, antibodies, and custom assay development services to complement these platforms.

EpiCypher continuously pushes technology boundaries to deliver innovative products, solutions, and services to epigenetics and chromatin biology researchers. Most recently, EpiCypher has been at the leading edge of chromatin mapping technology improvements with the recent launch of the highly sensitive epigenomic mapping CUTANA assays for ChIC, CUT&RUN, and CUT&Tag.

From our strong scientific expertise and rigor to our focus on customer success, EpiCypher is proud to be an epigenetics company For Scientists, By Scientists.

Featured Co-Authored Publications

Shah  et al.  (2018)

Molecular Cell

Examining the roles of H3K4 methylation states with systematically characterized antibodies

This study established SNAP-ChIP Recombinant Nucleosome Spike-ins as a robust and essential technology for defining histone PTM antibody binding in ChIP experiments. Direct comparison of SNAP-ChIP (also known as ICeChIP) Spike-ins and histone peptide arrays revealed that modified histone peptides had no predictive ability for antibody performance in ChIP, and many “ChIP-grade” antibodies to H3K4me1, me2, and me3 exhibited off-target binding and poor pull-down efficiency. Instead, SNAP-ChIP Spike-in Controls were able to accurately characterize antibody performance within the context of a ChIP assay.

Yusufova  et al.  (2021)

Nature

Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture

Although linker H1 histone proteins are often mutated in B-cell lymphoma, the downstream impacts of these mutant alleles are not well known. In this study, Yusufova et al. demonstrate that H1 histones are bona fide tumor suppressor proteins, which are required to package early developmental genes into transcriptionally inaccessible heterochromatin. EpiCypher CUTANA CUT&RUN assays were key for analyzing changes in heterochromatin structure in rare germinal center B cells, as standard ChIP-seq assays lack the sensitivity to reliably profile from limited primary cell samples.

Weinberg  et al.  (2021)

Nature Genetics

Two competing mechanisms of DNMT3A recruitment regulate the dynamics of de novo DNA methylation at PRC1-targeted CpG islands

Aberrant DNA methylation at CpG islands (CGIs) occurs in many diseases, but the mechanism is still unclear. Here, we used dCypher binding assays to characterize DNMT3A proteins with disease-associated mutations, revealing novel binding preference for H2AK119ub dNucs. DNMT3A mutant cell lines accumulated DNA methylation at CGIs, which was dependent on H2AK119ub generated by the repressive PRC1 complex. Combined with Weinberg et al. 2019, our team has convincingly demonstrated the role of epigenetic crosstalk in regulating chromatin structure, gene expression, and disease development.

Weinberg  et al.  (2019)

Nature

H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape

Here, dCypher nucleosome panels illuminated the binding preference of chromatin reader DNMT3A towards NSD1-catalyzed H3K36me2, highlighting the importance of the nucleosome context when defining histone PTM interactions. Notably, alterations in each of these chromatin regulators results in childhood overgrowth syndromes (mutation of DNMT3A is associated with Tatton-Brown-Rahman syndrome, while changes in NSD1 cause Sotos syndrome). This work established a new regulatory link between the two growth disorders, as loss of NSD1 leads to misregulated localization of DNMT3A and altered DNA methylation in intergenic regions.

Thålin  et al.  (2020)

Journal of Thrombosis and Haemostasis

Quantification of citrullinated histones: Development of an improved assay to reliably quantify nucleosomal H3Cit in human plasma

Neutrophil extracellular traps (NETs) are webs of citrullinated nuclear proteins released during inflammatory processes and can be detected in human plasma by probing for histone H3 citrullination (H3Cit) on circulating nucleosomes. Although NETs have been linked to numerous human pathologies, their application in diagnostics has been limited due to a lack of reliable assays. Here, EpiCypher collaborated with Dr. Charlotte Thålin to develop a novel assay to quantify nucleosomal H3Cit from human plasma. EpiCypher dNucs were key to antibody validation and for generating a standard curve for accurate H3Cit quantification.

Schachner  et al.  (2021)

Nature Methods

Decoding the Protein Composition of Whole Nucleosomes with Nuc-MS

Mass spectrometry represents a powerful approach for characterization of the histone code. However, existing methods for mass spec of chromatin utilize bulk fragmented histones, greatly complicating the analysis of co-occurring histone PTMs within nucleosome subunits and obscuring cooperative functions. In this paper, EpiCypher collaborated with the Kelleher lab to develop Nuc-MS, a novel approach that enables detection of histone PTMs and variants within intact mononucleosomes. Nuc-MS was established using defined dNuc substrates from EpiCypher, providing robust validation for this breakthrough technology.

All Co-Authored Publications

To view all publications featuring EpiCypher products, click here.