The Nucleosome Remodeling and Deacetylase complex has an asymmetric, dynamic, and modular architecture

Abstract

The Nucleosome Remodeling and Deacetylase (NuRD) complex is essential for development in complex animals but has been refractory to biochemical analysis. We present the first integrated analysis of the architecture of the native mammalian NuRD complex, combining quantitative mass spectrometry, covalent cross-linking, protein biochemistry and electron microscopy. NuRD is built around a 2:2:4 pseudo-symmetric deacetylase module comprising MTA, HDAC and RBBP subunits. This module interacts asymmetrically with a remodeling module comprising one copy each of MBD, GATAD2 and CHD subunits. The previously enigmatic GATAD2 controls the asymmetry of the complex and directly recruits the ATP-dependent CHD remodeler. Unexpectedly, the MTA-MBD interaction acts as a point of functional switching. The transcriptional regulator PWWP2A modulates NuRD assembly by competing directly with MBD for binding to the MTA-HDAC-RBBP subcomplex, forming a 'moonlighting' PWWP2A-MTA-HDAC-RBBP complex that likely directs deacetylase activity to PWWP2A target sites. Taken together, our data describe the overall architecture of the intact NuRD complex and reveal aspects of its structural dynamics and functional plasticity. INO80(1, 2) and SWR1 complexes (3), as well as to the Snf2 (4) and Chromodomain-Helicase-DNA-binding 1 (CHD1) remodelers (5), our understanding of how such enzymes bring about remodeling is still underdeveloped. This is particularly true for the nucleosome remodeling and deacetylase (NuRD) complex.The NuRD complex is widely distributed among Metazoans and is expressed in most, if not all, tissues. It is essential for normal development (6, 7) and is a key regulator in the reprogramming of differentiated cells into pluripotent stem cells (8-10). Age-related reductions in NuRD subunit levels are strongly associated with memory loss, metastatic potential in human cancers (11), and the accumulation of chromatin defects (12, 13).The mammalian NuRD complex comprises at least six subunits (Figure S1a), and for each subunit there are at least two paralogues, giving the potential for significant compositional heterogeneity. CHD4 (and its paralogues CHD3 and -5) is the ATP-dependent DNA translocase in the complex and harbours several regulatory and targeting domains. For example, the PHD domains of CHD4 can recognize histone H3 N-terminal tails bearing methyllysine marks (14-16), and the HMG domain has been shown to bind to poly-ADP(ribose) (17). What distinguishes NuRD from many other remodelers is that it harbours a second catalytic activity, imparted by the histone deacetylases HDAC1 and -2. MBD2 and -3 can bind hydroxymethylated and/or methylated , and RBBP4 and -7 can each bind histone tails (21) and other transcriptional regulators (22,23). The metastasis-associated proteins MTA1, -2 and -3 contain several domains that are associated with nucleosome recognition, whereas GATAD2A and GATAD2B bind to both 25) and CHD proteins (25, 26) but otherwise do not have known functions. Some structural information is available for portions of t...

Molecular architecture of nucleosome remodeling and deacetylase sub-complexes by integrative structure determination

“…Considerable diversity is observed in subunit isoforms and NuRD-associated factors across tissues (Burgold et al, 2019; Denslow and Wade, 2007; Hoffmann and Spengler, 2019). NuRD comprises two catalytic modules - a histone deacetylase module and ATP-dependent chromatin-remodeling module (Burgold et al, 2019; Denslow and Wade, 2007; Low et al, 2020). The deacetylase module contains metastasis-associated proteins (MTA1/2/3) that form a dimeric scaffold for the histone deacetylases (HDAC1/2).…”

“…It also contains the chaperones RBBP4/7, which mediate interactions of NuRD with histone tails and transcription factors (Basta and Rauchman, 2017, 2015; Hong et al, 2005). The chromatin-remodeling module contains methyl-CpG DNA binding proteins (MBD2/3) that recruit NuRD to methylated and/or hemi-methylated DNA, GATA-type zinc-finger proteins (GATAD2A/B), and an ATP-dependent DNA translocase (CHD3/4/5) (Burgold et al, 2019; Low et al, 2020).…”

“…Several attempts made to determine the stoichiometry of the endogenous NuRD complex have returned variable results (Bode et al, 2016; Guo et al, 2019; Kloet et al, 2015; Sharifi Tabar et al, 2019; Smits et al, 2013; Spruijt et al, 2016; Zhang et al, 2016). A recent characterization by quantitative mass spectrometry from (Low et al, 2020) reported a 2:2:4:1:1:1 (MTA1:HDAC1:RBBP4:MBD3:GATAD2A:CHD4) stoichiometry for the full NuRD complex. Atomic structures of parts of the NuRD complex, including the MTA1-HDAC1 dimer, RBBP4 bound to MTA1, the MBD domain of MBD3, and the coiled-coil dimer of MBD2 and GATAD2A have been determined by X-ray crystallography and NMR spectroscopy (Alqarni et al, 2014; Cramer et al, 2014; Gnanapragasam et al, 2011; Millard et al, 2016, 2013).…”

“…Atomic structures of parts of the NuRD complex, including the MTA1-HDAC1 dimer, RBBP4 bound to MTA1, the MBD domain of MBD3, and the coiled-coil dimer of MBD2 and GATAD2A have been determined by X-ray crystallography and NMR spectroscopy (Alqarni et al, 2014; Cramer et al, 2014; Gnanapragasam et al, 2011; Millard et al, 2016, 2013). Structures of the 2:2 MTA1-HDAC1 dimer, the 2:2:4 MTA1-HDAC1-RBBP4 complex (MHR), the 2:2:2 MTA1 N -HDAC1-MBD3 GATAD2CC (MHM) complex, the 2:2:4:1:1 MTA1-HDAC1-RBBP4-MBD3-GATAD2 (NuDe complex), and CHD4 bound to a nucleosome substrate have also been characterized at various resolutions by negative stain and/or cryo-electron microscopy (Farnung et al, 2020; Low et al, 2020; Millard et al, 2020, 2016).…”

“…Pairwise interactions between domains and subunits within the MHR, MHM, NuDe, and the endogenous NuRD complexes have also been characterized by chemical crosslinking and mass spectrometry (XLMS) (Low et al, 2020; Millard et al, 2016). A model of the MHM complex, based on crosslinks-driven rigid-body docking of known atomic structures with a pair of MTA1-RBBP4 structures manually placed, has also been reported (Low et al, 2020). While this represents the most complete model of NuRD architecture, it still only accounts for 30% of residues in the NuRD complex.…”