Towards elucidating the stability, dynamics and architecture of the nucleosome remodeling and deacetylase complex by using quantitative interaction proteomics

Kloet, Susan L.; Baymaz, H. Irem; Makowski, Matthew; Groenewold, Vincent; Jansen, Pascal W.T.C.; Berendsen, Madeleine R.; Niazi, Hassin; Kops, Geert J. P. L.; Vermeulen, Michiel

doi:10.1111/febs.12972

Cited by 89 publications

(108 citation statements)

References 41 publications

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“…To derive a scaling factor to account for the gel staining properties of each subunit, we took into account the NuRD: NuDe ratio calculated for each of these fractions above and also the number of copies of each subunit in the complex (derived from published stoichiometry data on the NuRD complex (31,32)). Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Next, the band intensity was measured by densitometry for each subunit in a SYPRO-Rubystained SDS-PAGE of each sucrose gradient fraction. Stoichiometry data for NuRD subunits from previous reports (31,32) were then averaged (giving RBBP:MTA:GATAD2:HDAC: MBD:CHD ratios of 4.4:2.1:1.6:1:1:0.75) and combined with the densitometry data using the following formula to calculate gel intensity scaling factors for the various NuRD components relative to HDAC1/2.…”

Section: Methodsmentioning

confidence: 99%

“…Stoichiometry data derived from label-free mass spectrometry measurements also provide hints about the number of copies of each subunit that come together in the complex (31,32), although the mass spectrometric data do not seem entirely consistent with the structural data. However, in contrast to the remodeling complexes described above, nothing is known about the overall architecture of the NuRD complex (Note added in proof).…”

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confidence: 93%

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CHD4 Is a Peripheral Component of the Nucleosome Remodeling and Deacetylase Complex

Low

Webb

Silva

et al. 2016

Journal of Biological Chemistry

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Chromatin remodeling enzymes act to dynamically regulate gene accessibility. In many cases, these enzymes function as large multicomponent complexes that in general comprise a central ATP-dependent Snf2 family helicase that is decorated with a variable number of regulatory subunits. The nucleosome remodeling and deacetylase (NuRD) complex, which is essential for normal development in higher organisms, is one such macromolecular machine. The NuRD complex comprises ϳ10 subunits, including the histone deacetylases 1 and 2 (HDAC1 and HDAC2), and is defined by the presence of a CHD family remodeling enzyme, most commonly CHD4 (chromodomain helicase DNA-binding protein 4). The existing paradigm holds that CHD4 acts as the central hub upon which the complex is built. We show here that this paradigm does not, in fact, hold and that CHD4 is a peripheral component of the NuRD complex. A complex lacking CHD4 that has HDAC activity can exist as a stable species. The addition of recombinant CHD4 to this nucleosome deacetylase complex reconstitutes a NuRD complex with nucleosome remodeling activity. These data contribute to our understanding of the architecture of the NuRD complex.Nucleosomes effectively act as a roadblock to all aspects of genome biology. ATP-dependent chromatin remodeling enzymes solve this problem by using ATP-derived energy to alter the positions, occupancy and composition of nucleosomes. All remodelers possess a highly related ATPase motor domain from the helicase family and are classified into four subfamilies (INO80, ISWI, SWR1, and CHD) based on sequence similarity (1). Each subfamily is represented in nearly all eukaryotes, suggesting that they catalyze different remodeling events. For example, ISWI proteins reposition (or slide) nucleosomes to create regularly spaced arrays; this periodic organization is a key characteristic of DNA at the start of genes (2). SWR1 and INO80 enzymes have opposing roles in histone variant dynamics; the former incorporates these histone variants (e.g. H2A.Z), whereas the latter removes them. These variants set up specific chromatin structures that modulate transcription and replication, although the roles of many variants are still under debate (3). Fundamentally, these remodeling enzymes all alter the accessibility of DNA to other DNA-binding factors and thereby broadly underpin genome biology.Remodelers frequently act in the context of large multisubunit complexes, and in general, the "mixing and matching" of complex composition can generate complexes with varying activities; the human ISWI protein Snf2h for instance has been identified in six distinct complexes (4). Likewise, the accessory subunits can also modulate remodeler activity. For example, the paralogous methyl-CpG-binding domain proteins 2 and 3 (MBD2 and MBD3) subunits of the nucleosome remodeling and deacetylase (NuRD) 6 complex are mutually exclusive (5); MBD2 recognizes 5-methylcytosine-modified DNA, whereas MBD3 instead binds to 5-hydroxymethylated DNA (6, 7). Unsurprisingly, it has been observed tha...

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 93%

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CHD4 Is a Peripheral Component of the Nucleosome Remodeling and Deacetylase Complex

Low

Webb

Silva

et al. 2016

Journal of Biological Chemistry

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“…We find that multiple genetic targets of BRD4-NUT or ZNF532-NUT, including ZNF532 and ZMYND8, encode components of BRD4 regulatory complexes. Interestingly, it was previously reported that ZMYND8/ZNF532/ZNF592/ZNF687 interact with each other as a central hub in a large transcriptional network (26,30). ZMYND8 has several important chromatin-binding domains (bromodomain, PWWP, PHD finger, MYND), and can function as a combinatorial reader of histone modifications such as H3K4me1 and H3K14ac (31).…”

Section: Discussionmentioning

confidence: 99%

“…5), including with ZMYND8, ZNF687, ZNF592, and BRD4. These proteins were also linked to ZNF532 in data from previous mass spectrometric analyses (26)(27)(28). Interestingly, the ZMYND8 locus, encoding a top interactor of ZNF532, is bound by NUT-fusion proteins in all NMC lines tested (selected examples are shown in Fig.…”

Section: Znf532-nut Forms Megadomains Of Hyperacetylated Chromatinmentioning

confidence: 96%

Ectopic protein interactions within BRD4–chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma

Alekseyenko

Walsh

Zee

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

111

167

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To investigate the mechanism that drives dramatic mistargeting of active chromatin in NUT midline carcinoma (NMC), we have identified protein interactions unique to the BRD4-NUT fusion oncoprotein compared with wild-type BRD4. Using cross-linking, affinity purification, and mass spectrometry, we identified the EP300 acetyltransferase as uniquely associated with BRD4 through the NUT fusion in both NMC and non-NMC cell types. We also discovered ZNF532 associated with BRD4-NUT in NMC patient cells but not detectable in 293T cells. EP300 and ZNF532 are both implicated in feed-forward regulatory loops leading to propagation of the oncogenic chromatin complex in BRD4-NUT patient cells. Adding key functional significance to our biochemical findings, we independently discovered a ZNF532-NUT translocation fusion in a newly diagnosed NMC patient. ChIP sequencing of the major players NUT, ZNF532, BRD4, EP300, and H3K27ac revealed the formation of ZNF532-NUT-associated hyperacetylated megadomains, distinctly localized but otherwise analogous to those found in BRD4-NUT patient cells. Our results support a model in which NMC is dependent on ectopic NUT-mediated interactions between EP300 and components of BRD4 regulatory complexes, leading to a cascade of misregulation.BioTAP-XL | hyperacetylation | ZNF532-NUT | topological domains | BRD4

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The NuRD complex and macrocephaly associated neurodevelopmental disorders

Pierson

Otero

Grand

et al. 2019

American J of Med Genetics Pt C

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The nucleosome remodeling and deacetylase (NuRD) complex is a major regulator of gene expression involved in pluripotency, lineage commitment, and corticogenesis. This important complex is composed of seven different proteins, with mutations in CHD3, CHD4, and GATAD2B being associated with neurodevelopmental disorders presenting with macrocephaly and intellectual disability similar to other overgrowth and intellectual disability (OGID) syndromes. Pathogenic variants in CHD3 and CHD4 primarily involve disruption of enzymatic function. GATAD2B variants include loss‐of‐function mutations that alter protein dosage and missense variants that involve either of two conserved domains (CR1 and CR2) known to interact with other NuRD proteins. In addition to macrocephaly and intellectual disability, CHD3 variants are associated with inguinal hernias and apraxia of speech; whereas CHD4 variants are associated with skeletal anomalies, deafness, and cardiac defects. GATAD2B‐associated neurodevelopmental disorder (GAND) has phenotypic overlap with both of these disorders. Of note, structural models of NuRD indicate that CHD3 and CHD4 require direct contact with the GATAD2B‐CR2 domain to interact with the rest of the complex. Therefore, the phenotypic overlaps of CHD3‐ and CHD4‐related disorders with GAND are consistent with a loss in the ability of GATAD2B to recruit CHD3 or CHD4 to the complex. The shared features of these neurodevelopmental disorders may represent a new class of OGID syndrome: the NuRDopathies.

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Towards elucidating the stability, dynamics and architecture of the nucleosome remodeling and deacetylase complex by using quantitative interaction proteomics

Cited by 89 publications

References 41 publications

CHD4 Is a Peripheral Component of the Nucleosome Remodeling and Deacetylase Complex

CHD4 Is a Peripheral Component of the Nucleosome Remodeling and Deacetylase Complex

Ectopic protein interactions within BRD4–chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma

The NuRD complex and macrocephaly associated neurodevelopmental disorders

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