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The dCypher Approach to Interrogate Chromatin Reader Activity Against Posttranslational Modification-Defined Histone Peptides and Nucleosomes

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Chromatin

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2458))

Abstract

Bulk chromatin encompasses complex sets of histone posttranslational modifications (PTMs) that recruit (or repel) the diverse reader domains of Chromatin-Associated Proteins (CAPs) to regulate genome processes (e.g., gene expression, DNA repair, mitotic transmission). The binding preference of reader domains for their PTMs mediates localization and functional output, and are often dysregulated in disease. As such, understanding chromatin interactions may lead to novel therapeutic strategies, However the immense chemical diversity of histone PTMs, combined with low-throughput, variable, and nonquantitative methods, has defied accurate CAP characterization. This chapter provides a detailed protocol for dCypher, a novel approach for the rapid, quantitative interrogation of CAPs (as mono- or multivalent Queries) against large panels (10s to 100s) of PTM-defined histone peptide and semisynthetic nucleosomes (the potential Targets). We describe key optimization steps and controls to generate robust binding data. Further, we compare the utility of histone peptide and nucleosome substrates in CAP studies, outlining important considerations in experimental design and data interpretation.

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Acknowledgments

This work was supported by US National Institutes of Health (NIH) grants (R44GM116584, R44GM117683 and R44CA214076) to EpiCypher.

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Authors and Affiliations

  1. EpiCypher Inc., Durham, NC, USA

    Matthew R. Marunde, Irina K. Popova, Ellen N. Weinzapfel & Michael-C. Keogh

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  1. Matthew R. Marunde
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  2. Irina K. Popova
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  3. Ellen N. Weinzapfel
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  4. Michael-C. Keogh
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Correspondence to Michael-C. Keogh .

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Editors and Affiliations

  1. Department of Pathology Dunedin School of Medicine, University of Otago, Dunedin, New Zealand

    Julia Horsfield

  2. Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht, The Netherlands

    Judith Marsman

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Marunde, M.R., Popova, I.K., Weinzapfel, E.N., Keogh, MC. (2022). The dCypher Approach to Interrogate Chromatin Reader Activity Against Posttranslational Modification-Defined Histone Peptides and Nucleosomes. In: Horsfield, J., Marsman, J. (eds) Chromatin. Methods in Molecular Biology, vol 2458. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2140-0_13

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