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Nat Biotechnol. 2020 Mar 2. doi: 10.1038/s41587-020-0434-2. [Epub ahead of print]

ChromID identifies the protein interactome at chromatin marks.

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Department of Molecular Mechanism of Disease, University of Zurich, Zurich, Switzerland.
Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland.
Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland.
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
Faculty of Science, University of Zurich, Zurich, Switzerland.
Department of Molecular Mechanism of Disease, University of Zurich, Zurich, Switzerland.


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.


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