The MTA1 subunit of the nucleosome remodeling and deacetylase complex can recruit two copies of RBBP4/7

Abstract

The nucleosome remodeling and deacetylase (NuRD) complex remodels the genome in the context of both gene transcription and DNA damage repair. It is essential for normal development and is distributed across multiple tissues in organisms ranging from mammals to nematode worms. In common with other chromatin-remodeling complexes, however, its molecular mechanism of action is not well understood and only limited structural information is available to show how the complex is assembled. As a step towards understanding the structure of the NuRD complex, we have characterized the interaction between two subunits: the metastasis associated protein MTA1 and the histone-binding protein RBBP4. We show that MTA1 can bind to two molecules of RBBP4 and present negative stain electron microscopy and chemical crosslinking data that allow us to build a low-resolution model of an MTA1-(RBBP4) 2 subcomplex. These data build on our understanding of NuRD complex structure and move us closer towards an understanding of the biochemical basis for the activity of this complex.

Refinement of the subunit interaction network within the nucleosome remodelling and deacetylase (NuRD) complex

“…Therefore, from this set of experiments it cannot be concluded that two RBBPs directly interact. In fact, we and others have demonstrated that MTA1 can simultaneously bind two molecules of RBBP4/7 [18, 19], indicating that the apparent RBBP-RBBP interaction is likely to be indirect – mediated by MTA1/2/3. We have observed a similar phenomenon when probing for other interactions between pairs of subunits, including CHD4 and RBBP7 (Figure 3e).…”

“…4C shows pulldowns using the same proteins co-expressed in HEK293 cells. Using the RRL system, RBBP4 interacts with MTA2 (consistent with [17][18][19]) but not with GATAD2B, MBD3cc or the HDAC1 + MTA2N complex. In contrast, and in line with the previous section, RBBP4 appeared to interact with every subunit tested in the HEK293 pulldowns.…”

“…Subsequently they showed by negative-stain single-particle EM that a longer MTA1 polypeptide [MTA1(162–546)] allows the HDAC1-MTA1 dimer to bind two RBBP4 subunits in a 2:2:2 fashion (HDAC:MTA:RBBP; Figure 9b) [19]. We showed through multiple approaches including single-particle EM that MTA1(449–715) binds two RBBP molecules simultaneously (Figure 9b) [18]. …”

“…(b) Single-particle EM envelopes for the (HDAC1-MTA1-RBBP4) 2 sub-complex (PDB ID: 5FXY and EMDB ID: EMD-3399 ) [19] and the MTA1-(RBBP4) 2 subcomplex (EMDB ID: EMD-3431 ) [18]. The structures have been rendered as a reduced resolution envelope by applying a Gaussian filter in Chimera [36].…”

“…1). Structural data on subcomplexes of NuRD are becoming available [15][16][17][18][19], but no structure of the intact complex exists. Since 1998, a considerable body of subunit interaction data has been built up that relies on the methods described above.…”