Chemical Profiling of Proteins Interacting with DNA Structures in Live Cells

Time: 12:00 pm
day: Day One


DNA–protein interactions regulate critical biological processes. Identifying proteins that bind to specific, functional genomic loci is essential to understand the underlying regulatory mechanisms on a molecular level.

In this presentation I will describe our co-binding-mediated protein profiling (CMPP) strategy developed together with the University of Cambridge to investigate the interactome of DNA secondary structures in native chromatin.

CMPP involves cell-permeable, functionalized ligand probes that bind endogenous secondary structures such as G-quadruplexes (G4s) and subsequently crosslink to co-binding interacting proteins in situ. I will first illustrate the bioinformatics approaches that went into investigating the robustness of CMPP by proximity labelling of a G4 binding protein in vitro.

Employing this approach in live cells, we then identified hundreds of putative interacting proteins from various functional classes. Next, we confirmed a high binding affinity and selectivity for several newly discovered interactors in vitro, and we validated the functionally important candidate SMARCA4 in cellular chromatin using an independent approach.

This work provides a chemical strategy to map protein interactions to specific nucleic acid features and discover new epigenetic targets in living cells.