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ChromID identifies the protein interactome at chromatin marks
Rodrigo Villaseñor1, Ramon Pfaendler1, Christina Ambrosi1,2
1Department of Molecular Mechanism of Disease, University of Zurich, Zurich, Switzerland.
Nature Biotechnology
|March 4, 2020
Summary
Researchers developed engineered chromatin readers (eCRs) to identify proteins interacting with specific DNA and histone modifications. This method, ChromID, reveals protein networks at distinct chromatin states, including bivalently modified promoters.
Area of Science:
- Molecular Biology
- Epigenetics
- Proteomics
Background:
- Chromatin modifications are crucial for genome regulation, primarily by recruiting specific proteins.
- The precise protein composition associated with distinct chromatin marks remains incompletely understood.
- Understanding these interactions is key to deciphering gene regulation and cellular function.
Purpose of the Study:
- To develop novel tools for characterizing the protein interactome at specific chromatin modifications.
- To investigate the protein landscape associated with DNA methylation and key histone trimethylation marks (H3K4me3, H3K9me3, H3K27me3).
- To explore protein interactions at bivalently modified promoters.
Main Methods:
- Engineered chromatin readers (eCRs) were designed using natural protein domains selective for DNA methylation and H3K4me3, H3K9me3, H3K27me3.
- eCRs were validated in living mouse embryonic stem cells for binding specificity and localization.
- The ChromID method was established by fusing eCRs to a biotin ligase (BASU) for proximity-dependent biotinylation and subsequent proteomic analysis.
Main Results:
- Engineered chromatin readers demonstrated selective binding to target modifications in living cells.
- The ChromID method successfully identified chromatin-dependent protein interactomes at distinct epigenetic marks.
- Analysis of bivalently modified promoters using a dual-modification reader revealed their unique protein composition.
Conclusions:
- Engineered chromatin readers provide a versatile platform for probing chromatin states.
- ChromID is an effective method for mapping protein interaction networks in a chromatin-dependent manner.
- This approach offers a detailed view of protein composition at specific and complex chromatin modifications, advancing our understanding of epigenomic regulation.
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