Abstract
Structural and functional analyses of nucleosomes containing histone variant H2A.Z have drawn a lot of interest over the past few years. Important work in budding yeast has shown that H2A.Z (Htz1)-containing nucleosomes are specifically located on the promoter regions of genes, creating a specific chromatin structure that is poised for disassembly during transcription activation. The SWR1 complex is responsible for incorporation of Htz1 into nucleosomes through ATP-dependent exchange of canonical H2A-H2B dimers for Htz1-H2B dimers. Interestingly, the yeast SWR1 complex is functionally linked to the NuA4 acetyltransferase complex in vivo. NuA4 and SWR1 are physically associated in higher eukaryotes as they are homologous to the TIP60/p400 complex, which encompasses both histone acetyltransferase (Tip60) and histone exchange (p400/Domino) activities. Here we present work investigating the impact of NuA4-dependent acetylation on SWR1-driven incorporation of H2A.Z into chromatin. Using in vitro histone exchange assays with native chromatin, we demonstrate that prior chromatin acetylation by NuA4 greatly stimulates the exchange of H2A for H2A.Z. Interestingly, we find that acetylation of H2A or H4 N-terminal tails by NuA4 can independently stimulate SWR1 activity. Accordingly, we demonstrate that mutations of H4 or H2A N-terminal lysine residues have similar effects on H2A.Z incorporation in vivo, and cells carrying mutations in both tails are nonviable. Finally, depletion experiments indicate that the bromodomain-containing protein Bdf1 is important for NuA4-dependent stimulation of SWR1. These results provide important mechanistic insight into the functional cross-talk between chromatin acetylation and ATP-dependent exchange of histone H2A variants.
Highlights
Maintenance by controlling access to DNA and signaling local regions for specific molecular interactions [1, 2]
Such cooperation between histone acetylation and ATPdependent exchange of histone H2A-H2B dimers is further supported by the fact that Drosophila and human NuA4 histone acetyltransferase (HAT) complexes contain subunits homologous to those found in the yeast SWR1 complex, including p400 [23,24,25, 31, 35]
It was shown that the Drosophila TIP60/p400 complex is able to exchange histone H2Av-H2B dimers on chromatin in vitro and that this reaction was stimulated by prior Tip60-dependent acetylation of histone H2Av [23]
Summary
Yeast Strains—Genomic SWR1 was fused to three copies of the FLAG epitope in BY4741 using PCR and p3XFLAGKanMX6 as template [40]. For the Bdf depletion experiment, SWR1 complex was FLAG-purified from Swr1FLAG/Bdf1-TAP whole cell extracts, and the purified material was incubated with the same ratio of IgG-Sepharose beads. A total of 40 ng of DNA equivalents of di/trinucleosomes immobilized on streptavidin-coupled magnetic beads were preincubated with 15 l of SWR1 complex in 50 l of exchange buffer (25 mM HEPES-KOH, pH 7.6, 0.1 mM EDTA, 5 mM MgCl2, 10% glycerol, 0.02% Nonidet P-40, 1 mM dithiothreitol, 0.1 mg/ml bovine serum albumin, and 70 mM KCl) for 30 min at 37 °C. For the NuA4 pre-acetylation step, the beads were first incubated with NuA4 and acetyl-CoA (0.15 mM) for 30 min at 37 °C followed by 2 washes with exchange buffer before adding the SWR1 complex. The two complexes share four subunits, Eaf2/Swc, Yaf, Arp, and Act, and Eaf has homology with parts of Swr1 [31]
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