The stoichiometry and interactome of the Nucleosome Remodeling and Deacetylase (NuRD) complex are conserved across multiple cell lines

Abstract

The nucleosome remodelling and deacetylase complex (NuRD) is a widely conserved regulator of gene expression. The determination of the subunit composition of the complex and identification of its binding partners are important steps towards understanding its architecture and function. The question of how these properties of the complex vary across different cell types has not been addressed in detail to date. Here, we set up a two‐step purification protocol coupled to liquid chromatography‐tandem mass spectrometry to assess NuRD composition and interaction partners in three different cancer cell lines, using label‐free intensity‐based absolute quantification (iBAQ). Our data indicate that the stoichiometry of the NuRD complex is preserved across our three different cancer cell lines. In addition, our interactome data suggest ZNF219 and SLC25A5 as possible interaction partners of the complex. To corroborate this latter finding, in vitro and cell‐based pull‐down experiments were carried out. These experiments indicated that ZNF219 can interact with RBBP4, GATAD2A/B and chromodomain helicase DNA binding 4, whereas SLC25A5 might interact with MTA2 and GATAD2A.

Cross‐linking mass spectrometry reveals the structural topology of peripheral NuRD subunits relative to the core complex

“…This loss of interaction with CDK2AP1 is most likely caused by deletion of the direct interaction domain. Upon closer inspection of the cross-links between GATAD2A and CHD proteins it is clear that this interaction also requires the C-terminus of the CHD proteins, which is in agreement with data published by the Mackay lab [13,26]. This may explain why the CHD4 1-1627 protein fails to interact with any NuRD complex subunit.…”

LncRNA HOTAIR promotes the invasion and metastasis of oral squamous cell carcinoma through metastasis‐associated gene 2

“…In this study, MTA2 is first identified as a possible target of HOTAIR–miR‐326 regulatory axis in OSCC. MTA2 serves as an important member of the MTA family and contains transcriptional corepressors that function in histone deacetylation 21 . MTA2 is also a component of the Twist complex which inhibits the expression of E‐cadherin 23 .…”

“…MTA2 is an important component of the nucleosome remodeling and deacetylase complex, which is conserved across various cell lines and is verified to promote EMT and progression of multiple carcinomas. 21,22 MTA2 is also a part of the Twist complex which can suppress the expression of E-cadherin, 23 and the knockdown of MTA2 inhibits invasion and metastasis of several cancers. 24,25 Therefore, MTA2 may act as a possible set of master coregulatory molecules in OSCC.…”

“…MTA2 serves as a vital member of the MTA family and contains transcriptional corepressors that are involved in histone deacetylation. MTA2 is an important component of the nucleosome remodeling and deacetylase complex, which is conserved across various cell lines and is verified to promote EMT and progression of multiple carcinomas 21,22 . MTA2 is also a part of the Twist complex which can suppress the expression of E‐cadherin, 23 and the knockdown of MTA2 inhibits invasion and metastasis of several cancers 24,25 .…”

GFI1 tethers the NuRD complex to open and transcriptionally active chromatin in myeloid progenitors

“…The proteins Rbbp7 and Rbbp4 bind histone H4 and most likely have roles as scaffolds (Kloet et al, 2015;Schmidberger et al, 2016). The GATA zinc-finger domain-containing proteins GATAD2A and -B directly interact with MBD2/3 and are also canonical members of the NuRD complex, although their precise function remains to be determined (Sharifi Tabar et al, 2019).…”