title: 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 (swr1Delta) 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 swr1Delta 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.
authors.affiliation: Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.
authors.forename: Takahito
authors.initials: T
authors.lastname: Yoshida
authors.forename: Kenji
authors.initials: K
authors.lastname: Shimada
authors.forename: Yukako
authors.initials: Y
authors.lastname: Oma
authors.forename: Véronique
authors.initials: V
authors.lastname: Kalck
authors.forename: Kazumi
authors.initials: K
authors.lastname: Akimura
authors.forename: Angela
authors.initials: A
authors.lastname: Taddei
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Iwahashi
authors.forename: Kazuto
authors.initials: K
authors.lastname: Kugou
authors.forename: Kunihiro
authors.initials: K
authors.lastname: Ohta
authors.forename: Susan M
authors.initials: SM
authors.lastname: Gasser
authors.forename: Masahiko
authors.initials: M
authors.lastname: Harata
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism*; D015870:Gene Expression; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D008840:Microfilament Proteins / Q000235:genetics / Q000378:metabolism*; D022022:Nuclear Pore / Q000378:metabolism*; D012269:Ribosomal Proteins / Q000235:genetics*
chemical_list: D002868:Chromosomal Proteins, Non-Histone; D006657:Histones; D008840:Microfilament Proteins; D012269:Ribosomal Proteins