ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner

The evolutionary conserved histone variant H2A.Z plays a crucial role in various DNA-based processes but the underlying mechanisms are not completely understood. Recently, we identified the zinc finger (ZNF) protein ZNF512B as an H2A.Z-, HMG20A- and PWWP2A-associated protein. Here, we report ZNF512B as a novel nucleosome remodeling and deacetylase (NuRD) complex binding protein. We discovered a conserved amino acid sequence within ZNF512B that resembles a NuRD-interaction domain (NIM) previously identified in FOG-1. By solving the crystal structure of this domain directly bound to the NuRD component RBBP4 and by applying several biochemical assays we demonstrate that this novel internal NIM sequence is both necessary and sufficient for high-affinity NuRD binding. Transcriptome analyses and reporter assays identify ZNF512B as regulator (repressor) of gene expression, in both NuRD-dependent and -independent modes. Surprisingly, high levels of ZNF512B expression lead to concomitant nuclear protein and chromatin aggregation foci that form independent of the interaction with the NuRD complex but depend on ZNF512B's zinc fingers. Our study has implications for diseases in which ZNF512B's expression is deregulated, such as cancer and neurodegenerative diseases and reveal the existence of more proteins as potential NuRD interactors. Overall design: To investigate the role of ZNF512B in the regulation of gene expression, we overexpressed GFP-ZNF512B (OE), together with GFP-ZNF512B_K423A (OE) mutant, and depleted ZNF512B (KD) by siRNA treatment in HeLaK cells, respectively. We then performed high-throughput RNA sequencing. Each experiment has at least two biological replicates. Differential gene expression analysis was performed in pair-wise conditions, that is GFP-ZNF512B OE vs GFP control, GFP-ZNF512B_K423A OE vs GFP control as well as ZNF512B KD vs siRNA scrambled control.