ArticleMethods in molecular biology (Clifton, N.J.)2022
The dCypher Approach to Interrogate Chromatin Reader Activity Against Posttranslational Modification-Defined Histone Peptides and Nucleosomes.
Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- PBRM1-dependent PBAF targeting is required for EMT and metastasis in breast cancer.Science advances · 2026Article
- Different modes of engagement with the nucleosome acidic patch yield distinct functional outcomes.Nucleic acids research · 2026Article
- Direct Readout of Multivalent Chromatin Reader-Nucleosome Interactions by Nucleosome Mass Spectrometry.ACS central science · 2026Article
- Different modes of engagement with the nucleosome acidic patch yield distinct functional outcomes.bioRxiv : the preprint server for biology · 2026Article
- Structural Genomics Defines PBRM1 Bromodomain Variant Function in ccRCC.Human mutation · 2026Article
- Nucleosome context regulates chromatin reader preference.Nucleic acids research · 2025Article
- A needed nomenclature for nucleosomes.Molecular cell · 2025Review
- Multivalent binding of the tardigrade Dsup protein to chromatin promotes yeast survival and longevity upon exposure to oxidative damage.Nature communications · 2025Article
- Histone H3 N-terminal recognition by the PHD finger of PHRF1 is required for proper DNA damage response.Nucleic acids research · 2025Article
- The CECR2 bromodomain displays distinct binding modes to select for acetylated histone proteins versus non-histone ligands.bioRxiv : the preprint server for biology · 2024Article
- Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.Nucleic acids research · 2024Article
- Article
- Readout of histone methylation by Trim24 locally restricts chromatin opening by p53.Nature structural & molecular biology · 2023Article
- An acetylation-mediated chromatin switch governs H3K4 methylation read-write capability.eLife · 2023Article
- Article
- A trivalent nucleosome interaction by PHIP/BRWD2 is disrupted in neurodevelopmental disorders and cancer.Genes & development · 2021Article
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Authors and funding
4 authors.
Funding
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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