The SnAC Domain of SWI/SNF Is a Histone Anchor Required for Remodeling

Abstract

The SWI/SNF chromatin remodeling complex changes the positions where nucleosomes are bound to DNA, exchanges out histone dimers, and disassembles nucleosomes. All of these activities depend on ATP hydrolysis by the catalytic subunit Snf2, containing a DNA-dependent ATPase domain. Here we examine the role of another domain in Snf2 called SnAC (Snf2 ATP coupling) that was shown previously to regulate the ATPase activity of SWI/SNF. We have found that SnAC has another function besides regulation of ATPase activity that is even more critical for nucleosome remodeling by SWI/SNF. We have found that deletion of the SnAC domain strongly uncouples ATP hydrolysis from nucleosome movement. Deletion of SnAC does not adversely affect the rate, processivity, or pulling force of SWI/SNF to translocate along free DNA in an ATP-dependent manner. The uncoupling of ATP hydrolysis from nucleosome movement is shown to be due to loss of SnAC binding to the histone surface of nucleosomes. While the SnAC domain targets both the ATPase domain and histones, the SnAC domain as a histone anchor plays a more critical role in remodeling because it is required to convert DNA translocation into nucleosome movement. The packing of DNA into chromatin involves the wrapping of 147 bp of DNA around a histone octamer to form a nucleosome and then assembly of nucleosomes into higher-order structures. Chromatin makes genomic DNA less accessible to protein factors important for transcription, replication, repair, and recombination. Chromatin structure is dynamic due to remodeling factors, some of which are ATP dependent, that facilitate making discrete regions accessible to other factors. ATP-dependent chromatin remodelers are single or large multisubunit assemblies composed of 1 to 17 subunits ranging from several kilodaltons to over a megadalton in molecular mass (1, 2). Each has a catalytic subunit with a conserved ATPase domain related to that of ATPdependent DNA helicases. In helicases, this domain couples ATP hydrolysis to DNA translocation and subsequent unwinding of double-stranded nucleic acid substrates by means of a translocase domain and a duplex destabilizing wedge domain (3-5). Unlike helicases, chromatin remodelers do not have nucleic acid unwinding activity, but have retained the translocase activity, which in turn repositions or disassembles nucleosomes (5, 6).Nucleosome movement by SWI/SNF-and ISWI-type complexes requires the ATPase domain to translocate along nucleosomal DNA near the dyad axis (7-10). DNA gaps near superhelical location 2 (SHL2) of the nucleosome block movement without interfering with binding of the remodeler. DNA translocation this far inside nucleosomes is challenging because there is no easy path for the ATPase domain to initially move. As the ATPase domain begins to translocate, it encounters histone-DNA interactions in both directions and has to overcome multiple histone-DNA interactions while trying to pull DNA into nucleosomes. The force required to disrupt histone-DNA interactions, as shown by mechanically ...

ATP-dependent chromatin remodeling during mammalian development

“…For example, the associated subunit IES2 in the INO80 complex activates the ATPase activity of the catalytic INO80 subunit, whereas two other subunits -IES6 and ARP5 -facilitate binding of the INO80 complex to nucleosomes . Similar modulation of the ATPase domain activity by other domains and associated subunits has been shown for SWI/SNF Sen et al, 2013) and ISWI (Clapier and Cairns, 2012;Hota et al, 2013) complexes. Furthermore, the assembly of tissue-specific isoforms of associated subunits into these complexes confers unique properties that are particularly suited to the tissue type and help in recruiting these complexes to tissuespecific regulatory genomic loci.…”

Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex

“…Interestingly, Mec1 and Snf2 interactions appear to occur between several functional domains of these proteins. For example, we discovered interactions between the kinase domain of Mec1 and the SnAC domain of Snf2 that regulates the ATPase domain of Snf2 and interacts with histones (Sen et al 2011(Sen et al , 2013. In fact, the cross-link between K1306 of Snf2 (SnAC domain) and K2318 of Mec1 is close to the active center of the Mec1 kinase domain, suggesting that the Snf2 SnAC domain physically interacts with the Mec1 kinase active center and could potentially regulate its activity.…”

Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent chromatin remodeling inhibition

“…BRG1 DLX1-binding domain 1 (837-916) localizes to a region known to contain mutations in CSS (Tsurusaki et al, 2012(Tsurusaki et al, , 2014; BRG1 DLX1-binding domain 2 (1247-1413) is highly conserved and overlaps the SNF2 ATP-coupling domain (SnAC; see Fig. 6A), a region known to be required for yeast SNF2 remodeling and histone binding (Sen et al, 2013). Thus, DLX1-BRG1 interactions have the potential to play a role in a neurodevelopmental disorder.…”