N Terminus of Swr1 Binds to Histone H2AZ and Provides a Platform for Subunit Assembly in the Chromatin Remodeling Complex

Abstract

Variant histone H2AZ-containing nucleosomes are involved in the regulation of gene expression. In Saccharomyces cerevisiae, chromatin deposition of histone H2AZ is mediated by the fourteen-subunit SWR1 complex, which catalyzes ATPdependent exchange of nucleosomal histone H2A for H2AZ. Previous work defined the role of seven SWR1 subunits (Swr1 ATPase, Swc2, Swc3, Arp6, Swc5, Yaf9, and Swc6) in maintaining complex integrity and H2AZ histone replacement activity. Here we examined the function of three additional SWR1 subunits, bromodomain containing Bdf1, actin-related protein Arp4 and Swc7, by analyzing affinity-purified mutant SWR1 complexes. We observed that depletion of Arp4 (arp4-td) substantially impaired the association of Bdf1, Yaf9, and Swc4. In contrast, loss of either Bdf1 or Swc7 had minimal effects on overall complex integrity. Furthermore, the basic H2AZ histone replacement activity of SWR1 in vitro required Arp4, but not Bdf1 or Swc7. Thus, three out of fourteen SWR1 subunits, Bdf1, Swc7, and previously noted Swc3, appear to have roles auxiliary to the basic histone replacement activity. The N-terminal region of the Swr1 ATPase subunit is necessary and sufficient to direct association of Bdf1 and Swc7, as well as Arp4, Act1, Yaf9 and Swc4. This same region contains an additional H2AZ-H2B specific binding site, distinct from the previously identified Swc2 subunit. These findings suggest that one SWR1 enzyme might be capable of binding two H2AZ-H2B dimers, and provide further insight on the hierarchy and interdependency of molecular interactions within the SWR1 complex.

Yeti, aDrosophila melanogasteressential gene, encodes a protein required for chromatin organization

“…The amount of YETI-GFP is unchanged in dom3/ dom3; Tub-Gal4/UAS-Yeti-GFP (lane 1) and dom3/+; Tub-Gal4/UAS-Yeti-GFP (lane 2) larvae (right panel). Wu et al, 2009;Morillo-Huesca et al, 2010). Our findings that H2A.V deposition is perturbed in Yeti mutants and that YETI interacts with both H2A.V and DOM-A (Fig.…”

NuA4-dependent Acetylation of Nucleosomal Histones H4 and H2A Directly Stimulates Incorporation of H2A.Z by the SWR1 Complex

“…It will be very important to investigate, using our in vitro assay, whether phospho-H2A in native chromatin is preferentially targeted by SWR1 for exchange with H2A.Z and whether acetylation of phospho-H2A by NuA4 specifically stimulates the reaction. It is intriguing to note that Arp4, a subunit shared by NuA4 and SWR1 and important for SWR1 histone exchange activity (26), was shown to interact with H2A C-terminal tail in vitro only when it carries the DNA damage inducible phosphorylation of serine 129 (54). This is certainly related to Tip60 function in the dynamics of ␥-H2A.X during DNA damage response in mammalian cells (51,57).…”

“…In addition, a recent report by Wu et al (26) further characterized the molecular determinants for SWR1 complex assembly and function. Intriguingly, this study demonstrates that Bdf1 association to SWR1 was dependent on the Arp4-Yaf9-Swc4-Act1 tetrameric subcomplex composed of the four subunits shared with the NuA4 complex.…”

Splice variants of the SWR1-type nucleosome remodeling factor Domino have distinct functions during Drosophila melanogaster oogenesis

“…Our comprehensive analysis revealed a specific involvement of DOM-B for the incorporation of H2A.V into chromatin at the global level. The N-termini of SWR1 and DOM-B harbor the HSA and ATPase spacer domains (Morrison and Shen, 2009), with interaction surfaces for further complex subunits (Billon and Côté, 2012;Gerhold and Gasser, 2014), and an additional H2A.Z-H2B dimer binding site (Wu et al, 2005(Wu et al, , 2009. Given the requirement for both isoforms for cell specification during oogenesis, we speculate that DOM-B might serve to incorporate bulk H2A.V into chromatin similar to SWR1, whereas DOM-A would be more involved in the regulatory refinement of location.…”