The NuRD architecture

Abstract

The nucleosome remodeling and deacetylase (NuRD) complex regulates chromatin organization, gene transcription, genomic stability and developmental signaling. NuRD has a unique dual enzymatic activity, containing an ATPase and a histone deacetylase among its six core subunits. Recent studies indicate that NuRD composition and the interplay between subunits may dictate the diverse functions of the complex. In this review, we examine the structures and biological roles of the NuRD subunits and discuss new avenues of research to advance our understanding of the NuRD-mediated signaling network.

Fig. 1

The NuRD complex and its core components. a Interactions between subunits and binding of the individual subunits to histones, DNA and other proteins or co-factors (Co-F). Co-F of CHD3/4: hunchback, Tramtrack69, KAP1, NAB2, RFP, E7, RORγ, Ikaros, Ki-1/57 and CGI-55; of MBD2: MIZF and FAK; of RBBP7/4: FOG-1, BCL11B and BRCA1; of MTA: BCL-6, BCL11B, oestrogen receptor α, NRIF3, MAT1, MICoA, LMO4 and FOG-1. b Domain architecture of each subunit

Fig. 2

The structural basis for ligand binding by the NuRD components CHD4, HDAC2 and MBD2. a Solution structure of the CHD4 PHD2 finger in complex with a H3K9me3 peptide (PDB: 2L75). b Crystal structure of HDAC2 in complex with a small molecule inhibitor N-(4-aminobiphenyl-3-yl)benzamide (PDB: 3MAX). c Solution structure of the MBD module of MBD2 bound to a methylated DNA fragment, derived from the ρ-globin promoter (PDB: 2KY8)

Fig. 3

The structural basis for ligand binding by the NuRD components RBBP7/4 and p66α. a Crystal structure of RBBP7 in complex with a H4 peptide (PDB: 3CFS). b Crystal structure of RBBP4 in complex with a FOG-1 peptide (PDB: 2XU7). c Solution structure of CR1 of p66α bound to the CC domain of MBD2 (PDB: 2L2L). Hydrophobic Ile, Val and Leu residues forming the coiled-coil interface are shown

Fig. 4

Models depicting NuRD complex recruitment and function. a The classic, static model of NuRD action shows association of the NuRD complex with inactive genes. Recruitment is typically depicted as resulting from direct interaction between a NuRD subunit and a transcriptional repressor. b A dynamic model for NuRD function shows NuRD as acting to maintain dynamic equilibrium of histone acetylation at an active gene, resulting in fine-tuning of gene expression