ChromID identifies the protein interactome at chromatin marks
| Autor: | Annika L. Gable, Stefan Butz, Philipp Voigt, Nina Schmolka, Rodrigo Villaseñor, Christian von Mering, Ruedi Aebersold, Thomas W. Sheahan, Joël Wirz, Ramon Pfaendler, Tuncay Baubec, Sara Giuliani, Christina Ambrosi, Elana Bryan, Christian Feller, Massimiliano Manzo |
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| Přispěvatelé: | University of Zurich, Baubec, Tuncay |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Proteomics
Proteome Protein domain Biomedical Engineering 2204 Biomedical Engineering Bioengineering Biology Applied Microbiology and Biotechnology DNA-binding protein Interactome Article Chromatin proteomics Histones 03 medical and health sciences Mice 0302 clinical medicine Protein Interaction Mapping 2402 Applied Microbiology and Biotechnology Animals Protein Interaction Maps Cells Cultured Embryonic Stem Cells 030304 developmental biology Epigenomics 0303 health sciences 1502 Bioengineering epigenetics Nuclear Proteins systems biology DNA Methylation 10226 Department of Molecular Mechanisms of Disease Chromatin Cell biology Histone 1313 Molecular Medicine DNA methylation 1305 Biotechnology biology.protein 570 Life sciences biology Molecular Medicine chromatin synthetic biology 030217 neurology & neurosurgery Biotechnology |
| Zdroj: | Villaseñor, R, Pfaendler, R, Ambrosi, C, Butz, S, Giuliani, S, Bryan, E, Sheahan, T W, Gable, A L, Schmolka, N, Manzo, M, Wirz, J, Feller, C, von Mering, C, Aebersold, R, Voigt, P & Baubec, T 2020, ' ChromID identifies the protein interactome at chromatin marks ', Nature Biotechnology, vol. 38, no. 6, pp. 728-736 . https://doi.org/10.1038/s41587-020-0434-2 Nature biotechnology Nature Biotechnology Nature Biotechnology, 38 |
| Popis: | Chromatin modifications regulate genome function by recruiting proteins to the genome. However, the protein composition at distinct chromatin modifications has yet to be fully characterized. In this study, we used natural protein domains as modular building blocks to develop engineered chromatin readers (eCRs) selective for DNA methylation and histone tri-methylation at H3K4, H3K9 and H3K27 residues. We first demonstrated their utility as selective chromatin binders in living cells by stably expressing eCRs in mouse embryonic stem cells and measuring their subnuclear localization, genomic distribution and histone-modification-binding preference. By fusing eCRs to the biotin ligase BASU, we established ChromID, a method for identifying the chromatin-dependent protein interactome on the basis of proximity biotinylation, and applied it to distinct chromatin modifications in mouse stem cells. Using a synthetic dual-modification reader, we also uncovered the protein composition at bivalently modified promoters marked by H3K4me3 and H3K27me3. These results highlight the ability of ChromID to obtain a detailed view of protein interaction networks on chromatin. The protein complexes associated with specific chromatin marks in living cells are identified using engineered binding proteins. |
| Databáze: | OpenAIRE |
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