Transcriptional regulation involves the concerted action of chromatin regulators, transcription factors and the basal transcription machinery. The two general types of chromatin regulators are chromatin remodelers, which reposition and restructure nucleosomes1
, and chromatin modifiers, which add or remove covalent marks from the histone proteins2
. These chromatin regulatory complexes work together to mark and move nucleosomes, which can either help silence or activate transcription, depending on the context. Remodelers bear a catalytic ATPase subunit required for ATP-dependent nucleosome repositioning1,3,4
, whereas modifier complexes bear one or more subunits with histone-modification potential2,5,6
. However, in both cases, most of the subunits of chromatin regulatory complexes are nonenzymatic. These attendant subunits are specialized for diverse tasks: targeting the complex to particular nucleosomes, enabling complex association with particular DNA binding proteins or other complexes, or helping to regulate enzymatic activity.
Intriguingly, actin and ARPs are among the associated subunits of certain chromatin-remodeling and chromatin-modifying complexes7–9
. ARPs have been studied extensively in the budding yeast Saccharomyces cerevisiae
, which contains ten ARPs10
. Four ARPs (ARPs 1, 2, 3 and 10) reside mainly in the cytoplasm and have clear roles in actin filament nucleation and cytoskeletal regulation. In contrast, the remaining six ARPs (ARPs 4, 5, 6, 7, 8 and 9) are nuclear. Remarkably, all nuclear ARPs are associated exclusively with chromatin-regulating complexes, including ATP-dependent nucleosome remodelers and certain histone acetyltransferase (HAT) complexes. ARPs and actin are stable and stoichiometric members of SWI-SNF11,12
and INO80 family14
remodelers but are absent in ISWI and CHD family remodelers. Actin and ARPs are also present in HAT complexes related to the yeast NuA4 complex, which is essential for histone H4 acetylation15,16
. In addition, human complexes that combine both HAT and remodeler activities, such as p400, also bear ARPs and actin17
. However, beyond these notable exceptions, most HAT complexes (such as SAGA, SAS and ADA) lack ARPs18,19
Each chromatin complex associates with particular nuclear ARP proteins. For example, both the yeast SWI-SNF complex and the paralogous RSC complex contain Arp7 and Arp9, but lack actin11,12
. Human orthologs bear the ARP BAF53 as well as actin itself 20
. Thus, SWI-SNF complexes can contain either two ARPs or an ARP–actin pair. Interestingly, remodelers of the SWR1 and INO80 families bear actin and multiple ARPs; SWR1 contains Arp4 and Arp6 (ref. 21
), whereas INO80 contains Arp4, Arp5 and Arp8 (ref. 14
). Thus, remodelers show both selectivity and diversity in their association with ARPs, but the basis for these properties has not been elucidated.
For yeast RSC and SWI-SNF, Arp7 and Arp9 function as obligate heterodimers22
, and in SWI-SNF they are bound to the catalytic subunit Snf2 (ref. 23
). Likewise, in human SWI-SNF, BAF53 and actin are tightly associated with the ATPase subunit BRG1 (ref. 20
). For Ino80, omission of a large region of the N terminus leads to the loss of Arp4, Arp8 and actin, as well as other subunits, raising the possibility of an ARP nucleation domain in this region24
. In addition, a large insertion in the ATPase domain of Swr1 (unique to INO80 and SWR1 family remodelers) is required for the association of Arp6, as well as five other subunits25
. These results established the association of ARPs with the ATPase subunit; however, the domain(s) that enables the association with particular ARPs was not defined. Two previous experiments suggested that ARPs or actin regulate the ATPase domain. First, actin binding drugs moderately reduce the DNA-dependent ATPase activity of human SWI-SNF20
. Second, the omission of ARP proteins from INO80 prevented DNA-dependent ATPase activity and DNA binding24
. However, the ARP proteins in the RSC complex show only modest levels of ATPase regulation22
, raising the possibility that different remodeler families might, to different extents, rely on ARP regulation. Regardless, these studies did not address the mechanism or domain relationships that enable ARP docking or ATPase regulation.
Our work addresses two central questions: how do ARPs and actin selectively associate with chromatin regulators, and what domain relationships are involved in enabling ATPase regulation by ARPs? We provide several lines of evidence that the HSA domain is the general binding platform for nuclear ARPs and actin. We also provide genetic evidence that the ARP–HSA module cooperates with two domains (termed post-HSA and protrusion 1) that are present together only in chromatin-remodeling ATPases that contain ARPs, providing a mechanistic framework for the regulation of the ATPase subunit.