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

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.Genetic information within the eukaryotic cell nucleus is organized in a highly conserved structural polymer, chromatin, which supports and controls crucial functions of the genome. Chromatin remodeling and post-translational modifications of histones are critical processes regulating genome expression and maintenance by controlling access to DNA and signaling local regions for specific molecular interactions (1, 2). Incorporation of different histone variants in specific chromosomal regions is also known to be associated with important biological processes controlling gene expression and genome integrity (3).A specific histone variant, H2A.Z, has been the focus of intense research over the past few years (4 -6). Delineation of its impact on nucleosome structure and stability and on gene expression has turned into a long-heated debate involving apparently contradicting experimental data. However, recent findings led to an emerging model that could partly reconcile these contradictions (7). Genome-wide analyses of H2A.Z localization in eukaryotes indicate that it is preferentially found on gene promoter/regulatory regions within nucleosomes flanking more accessible DNA sequences (8 -14). Importantly, H2A.Z is found within the promoters of inactive or weakly transcribed ge...

Phosphorylation of Histone H2A at Serine 95: A Plant-Specific Mark Involved in Flowering Time Regulation and H2A.Z Deposition

“…The loss-of-function pie1 mutant flowers early because PIE1 is required for the deposition of H2A.Z at FLC, MAF4, and MAF5 (Deal et al, 2007). NuA4, the only essential histone acetyltransferase complex in S. cerevisiae, acetylates the N-terminal tails of histones H4 and H2A, which directly stimulates the incorporation of H2A.Z by the SWR1 complex (Altaf et al, 2010). Yaf9 is a component of the NuA4 and SWR1 complexes, can bind histones H3 and H4 in vitro, and is required for histone variant H2A.Z deposition and for H2A.Z and H4 acetylation (Zhang et al, 2004;Altaf et al, 2010).…”

“…NuA4, the only essential histone acetyltransferase complex in S. cerevisiae, acetylates the N-terminal tails of histones H4 and H2A, which directly stimulates the incorporation of H2A.Z by the SWR1 complex (Altaf et al, 2010). Yaf9 is a component of the NuA4 and SWR1 complexes, can bind histones H3 and H4 in vitro, and is required for histone variant H2A.Z deposition and for H2A.Z and H4 acetylation (Zhang et al, 2004;Altaf et al, 2010). Our results show that Arabidopsis YAF9a is required for H4 acetylation and the deposition of H2A.Z at GI, indicating that Arabidopsis YAF9a might be the counterpart of yeast Yaf9 and that YAF9a is involved in chromatin and transcriptional regulation at GI.…”

“…These two complexes share four subunits, Yaf9, Swc4, Arp4, and Act1, which function together to regulate chromatin structure and gene transcription (Krogan et al, 2004;Zhang et al, 2004). Yaf9 is a YEAST domain protein, whichisevolutionarilyconservedinyeast,mammals,andplants.Inyeast, the Yaf9 components of the SWR1 and NuA4 complexes are required for geneexpression, H4acetylation,andHtz1replacement at specificgenes (Zhang et al, 2004;Wang et al, 2009;Altaf et al, 2010). There are two genes encoding Yaf9 in Arabidopsis: YAF9a (TAF14b) and YAF9b (TAF14).…”

Mutagenesis of pairwise combinations of histone amino-terminal tails reveals functional redundancy in budding yeast

“…For example, the lethal phenotype caused by quadruplet mutations of all four lysine residues (H4K5, 8,12,16) within the H4 N-tail, which cannot be recapitulated with any combination of triple mutations on the lysines, indicates the redundancy of all four lysine residues for cell viability (17). Furthermore, triple mutations on lysines within H4 N-tail (H4K5, 8,12) in combination with deletion of H3 N-tail, which carries five acetylatable lysines (H3K9, 14,18,23,27), causes cellular lethality (12). Similarly, double deletion of the H2A/H2B or of the H3/H4 N-tails is lethal (18,19).…”

Chemical “Diversity” of Chromatin Through Histone Variants and Histone Modifications

“…More recently, ANP32E was identified as another H2A.Z-specific chaperone that removes H2A.Z from enhancer regions in mammalian cells [53, 54•]. The Swr1 complex binds to acetylated histones in general to preferentially deposit H2A.Z at acetylated regions of the genome [55]. However, recent studies by Ranjan et al showed that recognition of a nucleosome-free region by the Swr1 complex was more efficient for its targeting to DNA than recognition of acetylated chromatin [56].…”