4DCellFate

Developing a global understanding of the PRC and NuRD complexes in stem cell differentiation and in disease

Towards elucidating the stability, dynamics and architecture of the NuRD complex using quantitative interaction proteomics — Vermeulen and collaborator labs (2014)

Susan L. Kloet, H. Irem Baymaz, Matthew Makowski, Vincent Groenewold, Pascal W.T.C. Jansen, Madeleine Berendsen,  Hassin Niazi, Geert J. Kops, and Michiel Vermeulen

The Nucleosome Remodeling and Deacetylase (NuRD) complex is an evolutionary conserved chromatin-associated protein complex. Although the subunit composition of the mammalian complex is fairly well characterized, less is known about the stability and dynamics of these interactions. Furthermore, detailed information regarding protein-protein interaction surfaces within the complex is largely still lacking. Here, we show that the NuRD complex interacts with a number of substoichiometric zinc finger-containing proteins. Some of these interactions are salt sensitive (ZNF512B, SALL4), whereas others (ZMYND8) are not. The stoichiometry of the core subunits is not affected by high salt, indicating that the core complex is stabilized by hydrophobic interactions. Interestingly, the RBBP4 and -7 proteins are sensitive to high non-ionic detergent concentrations during affinity purification. In a subunit exchange assay using SILAC labeled nuclear extracts, the RBBP4 and -7 proteins are identified as dynamic core subunits of the NuRD complex, consistent with their proposed role as histone chaperones. Finally, using cross-linking mass spectrometry, we uncover novel features of NuRD molecular architecture that complement our AP-MS/MS data. Altogether, these findings extend our understanding of MBD3/NuRD structure and stability.

FEBS J (2014)    doi: 10.1111/febs.12972    

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