NuRD-interacting protein ZFP296 regulates genome-wide NuRD localization and differentiation of mouse embryonic stem cells

Susan L Kloet,Marijke P Baltissen,Michiel Vermeulen,Rik G H Lindeboom,Ino D Karemaker,Lisa Van Voorthuijsen,Deepani W Poramba-Liyanage,Pascal W T C Jansen,Raghu R Edupuganti

doi:10.1038/s41467-018-07063-7

Abstract

The nucleosome remodeling and deacetylase (NuRD) complex plays an important role in gene expression regulation, stem cell self-renewal, and lineage commitment. However, little is known about the dynamics of NuRD during cellular differentiation. Here, we study these dynamics using genome-wide profiling and quantitative interaction proteomics in mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs). We find that the genomic targets of NuRD are highly dynamic during differentiation, with most binding occurring at cell-type specific promoters and enhancers. We identify ZFP296 as an ESC-specific NuRD interactor that also interacts with the SIN3A complex. ChIP-sequencing in Zfp296 knockout (KO) ESCs reveals decreased NuRD binding both genome-wide and at ZFP296 binding sites, although this has little effect on the transcriptome. Nevertheless, Zfp296 KO ESCs exhibit delayed induction of lineage-specific markers upon differentiation to embryoid bodies. In summary, we identify an ESC-specific NuRD-interacting protein which regulates genome-wide NuRD binding and cellular differentiation.

Highlights

The nucleosome remodeling and deacetylase (NuRD) complex plays an important role in gene expression regulation, stem cell self-renewal, and lineage commitment
ChIP-seq analysis of CHD4 identified a large number of peaks (7262) that did not overlap with MBD3, which is in agreement with recent data and suggests that these could be sites where CHD4 acts independently of NuRD13,18
NuRD binding sites that are shared between the two cell types are enriched for transcription start sites (TSS) and are marked with H3K4me[3] and H3K27ac in both embryonic stem cells (ESCs) and neural progenitor cells (NPCs), suggesting that these occur at the promoters of constitutively active genes (Fig. 1d, e)

Summary

Introduction

The nucleosome remodeling and deacetylase (NuRD) complex plays an important role in gene expression regulation, stem cell self-renewal, and lineage commitment. Little is known about the dynamics of NuRD during cellular differentiation We study these dynamics using genome-wide profiling and quantitative interaction proteomics in mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs). The nucleosome remodeling and deacetylase (NuRD) complex is an evolutionarily conserved chromatin-associated protein complex which regulates gene expression and plays a role in the DNA damage response[1,2,3]. Our data reveal that the genome-wide binding of MBD3/NuRD is highly dynamic during differentiation, with most ESC-specific binding occurring at promoters and enhancers. We identify ZFP296 as a stem cellspecific NuRD-interacting protein which regulates genome-wide NuRD localization and differentiation of ESCs

Methods

Results

Conclusion