Actin-Related Protein Arp6 Influences H2A.Z-Dependent and -Independent Gene Expression and Links Ribosomal Protein Genes to Nuclear Pores

Abstract

Actin-related proteins are ubiquitous components of chromatin remodelers and are conserved from yeast to man. We have examined the role of the budding yeast actin-related protein Arp6 in gene expression, both as a component of the SWR1 complex (SWR-C) and in its absence. We mapped Arp6 binding sites along four yeast chromosomes using chromatin immunoprecipitation from wild-type and swr1 deleted (swr1Δ) cells. We find that a majority of Arp6 binding sites coincide with binding sites of Swr1, the catalytic subunit of SWR-C, and with the histone H2A variant Htz1 (H2A.Z) deposited by SWR-C. However, Arp6 binding detected at centromeres, the promoters of ribosomal protein (RP) genes, and some telomeres is independent of Swr1 and Htz1 deposition. Given that RP genes and telomeres both show association with the nuclear periphery, we monitored the ability of Arp6 to mediate the localization of chromatin to nuclear pores. Arp6 binding is sufficient to shift a randomly positioned locus to nuclear periphery, even in a swr1Δ strain. Arp6 is also necessary for the pore association of its targeted RP promoters possibly through cell cycle-dependent factors. Loss of Arp6, but not Htz1, leads to an up-regulation of these RP genes. In contrast, the pore-association of GAL1 correlates with Htz1 deposition, and loss of Arp6 reduces both GAL1 activation and peripheral localization. We conclude that Arp6 functions both together with the nucleosome remodeler Swr1 and also without it, to mediate Htz1-dependent and Htz1-independent binding of chromatin domains to nuclear pores. This association is shown to have modulating effects on gene expression.

PolySUMOylation by Siz2 and Mms21 triggers relocation of DNA breaks to nuclear pores through the Slx5/Slx8 STUbL

“…ChIP with anti-HA or anti-MYC epitope-tagged strains was carried out as previously described (Yoshida et al 2010) with modifications described in the Supplemental Material. Absolute enrichment was calculated as follows: For each time point, the signal from a site near the HO DSB at MAT was normalized Figure 7.…”

Nuclear organization in genome stability: SUMO connections

“…Although there is no evidence yet showing that specific pores bind specific sets of genes, recent studies implicate nuclear pores in a range of cellular processes, well beyond their function in macromolecular transport. Notably, in budding yeast and Drosophila certain highly transcribed, and in some cases stress-induced, genes are associated with nuclear pores [11][12][13][14][15][16][17][18][19]. This association not only promotes efficient export of mRNAs through coupling of transcription with export [10,11,13,14], but also helps modulate transcript levels of some loci.…”

“…INO1 or HXK1, like X-linked genes in male flies, show a modest but reproducible increase in expression when allowed to associate with nuclear pores [12,15,19]. On the other hand, there are other genes, notably a set of yeast ribosomal biogenesis genes, whose expression levels are lower when they are associated with nuclear pores [11,18]. This subset of promoters has a particular constellation of regulators and their localization at the nuclear pore depends on the actin-related protein Arp6 [18].…”

“…On the other hand, there are other genes, notably a set of yeast ribosomal biogenesis genes, whose expression levels are lower when they are associated with nuclear pores [11,18]. This subset of promoters has a particular constellation of regulators and their localization at the nuclear pore depends on the actin-related protein Arp6 [18]. Reduced expression of the HSP26 gene also correlates with localization at pores [11].…”

The actin family member Arp6 and the histone variant H2A.Z are required for spatial positioning of chromatin in chicken cell nuclei.

“…Members of the actin family, which consists of actin and actin-related proteins (Arps), are essential components of some of these complexes (Chen and Shen, 2007;Dion et al, 2010;Meagher et al, 2009;Ohfuchi et al, 2006;Oma and Harata, 2011). Arp6 is predominantly localized in the nucleus and identified as an essential component of the SWR1/SRCAP chromatin remodeling complex (Mizuguchi et al, 2004;Wu et al, 2005;Yoshida et al, 2010), which catalyzes the replacement of nucleosomal histone H2A with the variant H2A.Z both in yeasts and vertebrates (Mizuguchi et al, 2004;Ruhl et al, 2006;Wong et al, 2007).…”