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Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange

Abstract

The histone variant H2AZ is incorporated preferentially at specific locations in chromatin to modulate chromosome functions. In Saccharomyces cerevisiae, deposition of histone H2AZ is mediated by the multiprotein SWR1 complex, which catalyzes ATP-dependent exchange of nucleosomal histone H2A for H2AZ. Here, we define interactions between SWR1 components and H2AZ, revealing a link between the ATPase domain of Swr1 and three subunits required for the binding of H2AZ. We discovered that Swc2 binds directly to and is essential for transfer of H2AZ. Swc6 and Arp6 are necessary for the association of Swc2 and for nucleosome binding, whereas other subunits, Swc5 and Yaf9, are required for H2AZ transfer but neither H2AZ nor nucleosome binding. Finally, the C-terminal α-helix of H2AZ is crucial for its recognition by SWR1. These findings provide insight on the initial events of histone exchange.

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Figure 1: Subunits required for integrity of the SWR1 complex.
Figure 2: Most nonessential subunits are required for functional replacement of Htz1.
Figure 3: SWR1 components required for Htz1 or nucleosome binding.
Figure 4: Swc2 binds to Htz1.
Figure 5: Bacterially expressed Swc2 binds Htz1.
Figure 6: Swr1 is a scaffold for the complex.
Figure 7: The M6 domain in Htz1 is crucial for binding to the SWR1 complex.
Figure 8: Summary of subunit interactions in the SWR1 complex.

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Acknowledgements

We thank X. Shen (University of Texas, M.D. Anderson Cancer Center) for the pHtz1-2Flag plasmid, T. Tsukiyama (Fred Hutchinson Cancer Research Center) for the yeast strain W1544-4C and the 3× Flag–tagging plasmid and J. Landry and H. Xiao for helpful discussions. This work was supported by the Intramural Research Program of the US National Cancer Institute.

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Correspondence to Carl Wu.

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Supplementary information

Supplementary Fig. 1

mRNA expression levels of SWC2, ARP6, SWC6 and HTZ1 in wild-type, swc2delta arp6Δ and swc6Δ mutant strains. (PDF 596 kb)

Supplementary Fig. 2

Protein sequence alignment of S. cerevisiae Swc2 and related proteins from S. pombe, D. melanogaster, M. musculus and H. sapiens. (PDF 2290 kb)

Supplementary Fig. 3

Association of multiple subunits with Swr1 N2 and ATPase/Insert domains are required for functional replacement of H2AZ in vitro. (PDF 280 kb)

Supplementary Fig. 4

An alignment of D. melanogaster H2AvD and S. cerevisiae Htz1 and H2A. (PDF 78 kb)

Supplementary Fig. 5

Purified bacterially expressed His6-tagged proteins used in protein interaction assays. (PDF 850 kb)

Supplementary Table 1

Yeast strains used in this study. (PDF 95 kb)

Supplementary Methods (PDF 110 kb)

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Wu, WH., Alami, S., Luk, E. et al. Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange. Nat Struct Mol Biol 12, 1064–1071 (2005). https://doi.org/10.1038/nsmb1023

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