Actin-related protein Arp6 influences H2A.Z-dependent and -independent gene expression and links ribosomal protein genes to nuclear pores.
Actin-related protein Arp6 influences H2A.Z-dependent and -independent gene expression and links ribosomal protein genes to nuclear pores.
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DOI：
10.1371/journal.pgen.1000910
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发表时间：
2010-04-15
期刊：
影响因子：
4.5
通讯作者：
Harata M
中科院分区：
文献类型：
--
作者：
Yoshida T;Shimada K;Oma Y;Kalck V;Akimura K;Taddei A;Iwahashi H;Kugou K;Ohta K;Gasser SM;Harata M
肌动蛋白相关蛋白是染色质重构体中普遍存在的成分，在酵母和人类之间都是保守的。我们研究了萌芽酵母肌动蛋白相关蛋白Arp6在基因表达中的作用，无论是作为SWR1复合体(SWR-C)的一个组成部分，还是在它不存在的情况下。我们利用野生型和swr1缺失(swr1Δ)细胞的染色质免疫沉淀，在4条酵母染色体上定位了arp6结合位点。我们发现大多数Arp6结合位点与SWR-C催化亚单位Swr1的结合位点以及SWR-C沉积的组蛋白H_2A变异体Htz1(H_2A.Z)的结合位点一致。然而，在核糖体蛋白(RP)基因的启动子着丝粒和一些端粒上检测到Arp6结合，这与Swr1和Htz1的沉积无关。鉴于RP基因和端粒都与核周相关，我们监测了Arp6介导染色质定位到核孔的能力。Arp6结合足以将一个随机定位的位点转移到核外围，即使在swr1Δ株中也是如此。Arp6对于其靶向RP启动子的孔结合也是必需的，可能是通过细胞周期依赖因子。Arp6的缺失，而不是Htz1的缺失，导致这些RP基因的上调。相反，GAL1的孔关联与Htz1沉积相关，Arp6的丢失降低了GAL1的激活和外周定位。我们得出结论，Arp6与核小体重构体Swr1一起或不与其一起发挥作用，介导染色质结构域与核孔的Htz1依赖和Htz1非依赖的结合。这种联系被证明对基因表达有调节作用。肌动蛋白及其结构相似的肌动蛋白相关蛋白(Arp)是核小体重塑复合体的主要成分。在这里，我们证明了出芽酵母Arp6具有独立于其催化染色质重塑伙伴Swr1的功能。Arp6与多个启动子和亚端粒区域结合，而Swr1不在这些区域结合，这种联系在缺乏完整SWR-C重塑复合体的菌株中增加。我们发现Arp6可以介导其结合的核糖体蛋白基因启动子与核膜的联系。Arp6的缺失导致这些核糖体蛋白基因的上调，但对半乳糖诱导的GAL1启动子具有相反的作用，它与Swr1和组蛋白H2A变异体H2A.Z结合在一起。的确，Arp6的缺失和核膜结合延迟了半乳糖诱导的GAL1的激活。Arp6的两个相反的功能与Arp6介导的不同锚定途径有关：一种是要求完整的SWR-C沉积H2A.Z，而第二种Arp6可能直接介导启动子与核孔篮的结合。在这两种情况下，Arp6都与染色质在间期核内的空间定位有关，这对表达具有功能影响。这确定了肌动蛋白相关蛋白的一种新功能。
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. Actin and the structurally similar actin-related proteins (ARPs) are major components of nucleosome remodeling complexes in the nucleus. Here we show that budding yeast Arp6 has functions independent of its catalytic chromatin remodeling partner, Swr1. Arp6 binds to multiple promoters and subtelomeric zones at which Swr1 does not bind, and this association increases in strains lacking an intact SWR-C remodeling complex. We show that Arp6 can mediate the association of the ribosomal protein gene promoters to which it binds, with the nuclear envelope. The loss of Arp6 led to an up-regulation of these ribosomal protein genes, yet had the opposite effect on the galactose-induced GAL1 promoter, where it binds together with Swr1 and the histone H2A variant H2A.Z. Indeed, loss of Arp6 and nuclear envelope binding delays galactose-induced activation of GAL1. The two opposing functions of Arp6 correlate with different pathways of anchoring mediated by Arp6: one requires that the intact SWR-C deposits H2A.Z, while in the second Arp6 may mediate promoter binding to nuclear pore baskets directly. In both cases, Arp6 is implicated in the spatial localization of chromatin within the interphase nucleus, which has functional consequences on expression. This identifies a novel function for actin-related proteins.
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