ChromID identifies the protein interactome at chromatin marks

Rodrigo Villaseñor, Ramon Pfaendler, Christina Ambrosi, Stefan Butz, Sara Giuliani, Elana Bryan, Thomas W. Sheahan, Annika L. Gable, Nina Schmolka, Massimiliano Manzo, Joël Wirz, Christian Feller, Christian von Mering, Ruedi Aebersold, Philipp Voigt, Tuncay Baubec*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Pages (from-to)728-736
Number of pages9
JournalNature Biotechnology
Volume38
Issue number6
DOIs
Publication statusPublished - 2 Mar 2020

Keywords

  • chromatin
  • epigenetics
  • synthetic biology
  • systems biology
  • Chromatin proteomics

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