While the core subunits of Polycomb group (PcG) complexes are well characterized, little is known about the dynamics of these protein complexes during cellular differentiation. We used quantitative interaction proteomics and genome-wide profiling to study PcG proteins in mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs). We found the stoichiometry and genome-wide binding of PRC1 and PRC2 to be highly dynamic during neural differentiation. Intriguingly, we observed a downregulation and loss of PRC2 from H3K27me3-marked chromatin during differentiation, whereas PRC1 was retained at these sites. Additionally, we found PRC1 at enhancer and promoter regions independent of PRC2 binding and H3K27me3. Finally, overexpression of NPC-specific PRC1 interactors in ESCs led to increased Ring1b binding to and decreased expression of NPC-enriched Ring1b target genes. In summary, our integrative analyses have uncovered dynamic PcG subcomplexes and widespread co-localization with active chromatin marks during differentiation.

Highlights d Integrative proteomic analysis of the mouse ground-state pluripotent epigenome d Ground-state pluripotency is characterized by highly abundant PRC2 and H3K27me3 d PRC2 protects 2i ESCs from primed-like features such as DNA methylation d The pluripotent ground state is independent of both H3K27me3 and DNA methylation

Background: The NuRD complex controls gene expression through altering chromatin structure.Results: The MTA1-RbAp48 structure shows how the RbAp46/p48 histone chaperones are recruited to NuRD.Conclusion: The MTA subunits act as scaffolds for NuRD complex assembly.Significance: The MTA/RbAp48 interaction prevents binding of histone H4, which is crucial for understanding the role of the RbAp46/p48 chaperones in the complex.