Genomic DNA is complexed with histones and non-histone proteins to form chromatin, which is organized into active and inactive domains within the interphase nucleus 
. Histone tail modifications, chromatin compaction, and the subnuclear positioning of chromatin domains contribute epigenetic information that helps to determine gene expression patterns. While the enzymology of histone modification has been well characterized, little is known about the mechanisms that determine the spatial organization of chromatin in interphase nuclei.
In both vertebrates and yeast, transcriptionally inactive heterochromatin is enriched around the nucleolus or at the nuclear envelope (NE). In vertebrates, perinuclear anchoring appears to require the nuclear lamina, while in yeast integral proteins of the inner nuclear membrane tether repressed chromatin domains peripherally [reviewed in 4]
. Recent work has shown that in addition to silent heterochromatic loci, some euchromatic yeast genes are found at the NE as well. Indeed, inducible budding yeast genes such as INO1
, and HXK1
form a stable association with the nuclear pore complex (NPC) upon activation. In some cases, this interaction ensures maximal expression and fine-tuning of induction rates 
. The up-regulated X chromosome in male flies may also be associated with nuclear pores 
, as are the highly transcribed ribosomal protein (RP) genes of yeast 
Besides nuclear pore proteins, little is known about the components that position active chromatin domains within the nucleus. Nuclear actin and myosin, as well as myosin-like and actin-related proteins have been proposed as candidates that could contribute to the organization of transcription in the interphase nucleus 
. Indeed, actin itself is not only found as part of the filamentous cytoskeleton, but in various large chromatin modifying complexes, which are exclusively nuclear.
In all organisms from yeast to man, the actin family includes a number of proteins that are structurally similar to actin, called actin-related proteins or ARPs. The yeast S. cerevisiae
alone harbors ten ARP
genes, numbered from 1 to 10, with ascending degrees of dissimilarity to actin 
. Arp1-3 and Arp10 are cytoplasmic and help regulate cytoskeletal structures, while the other six (Arp4 to Arp9) are nuclear proteins 
. Nuclear ARPs, like nuclear actin, are often found in ATP-dependent chromatin modifying complexes that shift or displace nucleosomes, or in complexes that acetylate histone tails (e.g. NuA4 complex) [reviewed in 23]
. Exactly how ARPs contribute to nucleosome modification, however, is unknown.
Arp6 is an evolutionarily conserved nuclear ARP 
. The budding yeast Arp6, along with two other actin-family members, Act1 and Arp4, are part of the 14-component SWR1 chromatin remodeling complex (SWR-C), which is called SRCAP or Snf2-Related CREB-binding Activator Protein in mammals 
. In addition to the ATPase subunit, Swr1, SWR-C includes Swc1/Fun36, Swc2/Vps72, Swc3, Swc4/God1, Swc5/Aor1, Swc6/Vps71, Swc7, Yaf9, Bdf1, Rvb1, and Rvb2 
. The SWR-C holocomplex can exchange H2A with its variant H2A.Z (Htz1 in budding yeast) in assembled nucleosomes 
. Arp6 appears to form a subcomplex with Swc2, Swc3, and Swc6, and helps bridge this subcomplex with a second one containing Swr1, to form the functional SWR-C 
. Since Swc2 component is responsible for binding Htz1, the Arp6-mediated bridging is necessary for Htz1 deposition 
Nucleosomes containing acetylated H2A.Z are specifically enriched at promoters in higher eukaryotes, and consistently, Htz1 is found in nucleosomes flanking the nucleosome-free region located at transcription start sites in yeast 
. Additionally, Htz1 prevents the spreading of heterochromatin proteins in subtelomeric domains 
. In vitro
analyses have indicated that Arp6 contributes to transcriptional regulation by mediating Htz1 deposition 
, yet empirical evidence probing Arp6 function in vivo
is very limited.
In addition to a role in chromatin modulating complexes, some nuclear ARPs are thought to have functions beyond that of the remodeling complex to which they belong. In other cases, such as Arp4 (BAF53 in mammals), ARP proteins are involved in multiple complexes, so that the phenotypes associated with ARP
gene deletion are more extensive than those provoked by loss of a complex-specific ATPase subunit. Indeed, ARP4
is essential for viability in yeast, and the protein is a component of both INO80- and SWR-C remodeling complexes and the NuA4 histone acetyltransferase, which carry out distinct nuclear functions 
. Intriguingly, biochemical fractionation suggests that even these three complexes do not account for the entire nuclear complement of Arp4 
. Other support for independent functions for ARPs comes from genome-wide screens for synthetic lethality. The 125 gene deletions that are lethal for cells lacking Arp6, for instance, are not necessarily lethal for cells lacking the Swr1 ATPase subunit 
. Finally, the human Arp8 (hArp8) was implicated in mitotic chromosome phenotypes that could not be attributed to the hINO80 chromatin remodeling complex to which it belongs 
Here we have localized Arp6 along budding yeast chromosomes, both in the absence and presence of Swr1. We find that most Arp6 co-localizes with Swr1, being enriched in the promoters of divergently transcribed genes. This correlates with the deposition of the histone H2A variant H2A.Z/Htz1, and is consistent with the proposal that Arp6, as part of SWR-C, contributes to transcriptional regulation by exchanging H2A for Htz1 
. Intriguingly, however, Arp6 binds some promoters in a Swr1-independent manner, including promoters of ribosomal protein genes. Indeed, transcript measurements show that Arp6 alters RP gene regulation independently of Swr1-mediated Htz1 deposition. We find that Arp6 can relocate chromatin to the NE independently of Swr1, and that arp6
deletion reduces the association of RP genes with the NPC. This leads to a slight elevation in RP gene expression. We argue that Arp6 not only modulates local chromatin organization by facilitating Htz1 deposition, but also contributes to long-range chromatin organization that can fine-tune expression levels independently of SWR-C.