Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation

Abstract

Chromatin can be modified by posttranslational modifications of histones, ATP-dependent remodeling, and incorporation of histone variants. The Saccharomyces cerevisiae protein Yaf9 is a subunit of both the essential histone acetyltransferase complex NuA4 and the ATP-dependent chromatin remodeling complex SWR1-C, which deposits histone variant H2A.Z into euchromatin. Yaf9 contains a YEATS domain, found in proteins associated with multiple chromatin-modifying enzymes and transcription complexes across eukaryotes. Here, we established the conservation of YEATS domain function from yeast to human, and determined the structure of this region from Yaf9 by x-ray crystallography to 2.3 Å resolution. The Yaf9 YEATS domain consisted of a ␤-sandwich characteristic of the Ig fold and contained three distinct conserved structural features. The structure of the Yaf9 YEATS domain was highly similar to that of the histone chaperone Asf1, a similarity that extended to an ability of Yaf9 to bind histones H3 and H4 in vitro. Using structure-function analysis, we found that the YEATS domain was required for Yaf9 function, histone variant H2A.Z chromatin deposition at specific promoters, and H2A.Z acetylation.

Maintenance of Heterochromatin Boundary and Nucleosome Composition at Promoters by the Asf1 Histone Chaperone and SWR1-C Chromatin Remodeler in Saccharomyces cerevisiae

“…In agreement with published data, the yaf9DH3K56R strain had significantly reduced growth fitness compared to either of the single mutants alone, while the yaf9DH3K56Q strain did not display a strong growth defect ( Figure 6C) (Wang et al 2009). Furthermore, similar experiments testing for H3K9 acetylation, which is also mediated by Rtt109, revealed that the genetic interaction was specific to Asf1's role in H3K56 acetylation and not Rtt109-mediated H3K9 acetylation ( Figure S3).…”

“…Yeast lacking both ASF1 and YAF9 have an exacerbated growth defect compared to cells with a single deletion of either gene, suggesting these genes share a redundant function ( Figure 1) (Wang et al 2009). Given that YAF9 is required for H2A.Z deposition by SWR1-C, we asked if the synthetically sick phenotype of asf1Dyaf9D double mutants broadly reflected defects in SWR1-C function.…”

“…Because we previously demonstrated that H3K56ace-containing promoters preferentially lose H2A.Z in a yaf9 hypomorph, we next addressed whether H3K56 acetylation and Asf1 are involved in H2A.Z occupancy at gene promoters (Wang et al 2009). We used ChIP-qPCR to assay H2A.Z localization at the promoters of heterochromatin-proximal genes in strains that contain either asf1D or the H3K56R nonacetylable mutation.…”

“…For instance, at a subset of telomeres, the Yaf9 shared subunit is vital to H2A.Z incorporation, H4 acetylation, and proper telomere-specific gene expression changes (Zhang et al 2004;Wang et al 2009). Yaf9 contains an evolutionary conserved YEATS domain, whose closest structural relative in budding yeast is Asf1 (Wang et al 2009). These two proteins share a common essential function, although the nature thereof has yet to be defined.…”

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

“…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).…”