Structure of the RSC complex bound to the nucleosome

Abstract

The RSC complex remodels chromatin structure and regulates gene transcription. We used cryo–electron microscopy to determine the structure of yeast RSC bound to the nucleosome. RSC is delineated into the adenosine triphosphatase motor, the actin-related protein module, and the substrate recruitment module (SRM). RSC binds the nucleosome mainly through the motor, with the auxiliary subunit Sfh1 engaging the H2A-H2B acidic patch to enable nucleosome ejection. SRM is organized into three substrate-binding lobes poised to bind their respective nucleosomal epitopes. The relative orientations of the SRM and the motor on the nucleosome explain the directionality of DNA translocation and promoter nucleosome repositioning by RSC. Our findings shed light on RSC assembly and functionality, and they provide a framework to understand the mammalian homologs BAF/PBAF and the Sfh1 ortholog INI1/BAF47, which are frequently mutated in cancers.

Structural insights into assembly and function of the RSC chromatin remodeling complex

“…Fig. 6 RSC SAR complex and does not require a full complement of RSC subunits, as has been proposed 22 . Additionally, previous biochemical analysis has shown that mutation of several basic residues in the N-lobe of Snf2, which lies in close proximity to the exit site DNA, reduces the remodeling rate of the isolated Snf2 enzyme 19 .…”

“…Although this observation may also be due to the individual processing pipelines used in each study or reflect differences between Snf2 and Sth1, mutations in the Snf2 N-lobe near the exit site DNA severely reduce the ability of the isolated enzyme to remodel nucleosomes, supporting the idea that peeling is an intrinsic property of the ATPase domain 19 . Since other RSC subunits have also been shown to interact with the exit site DNA 21,22 , it is likely that multiple components of the full complex act in this process.…”

“…5a, yellow circle). Several studies have recently reported that SWI/SNF remodelers engage the acidic patch on the opposite face of the nucleosome using their Sfh1 (RSC) or Snf5 (SWI/SNF) subunit (Fig 7e) [20][21][22]24,24 . This interaction is vital to the function of the enzyme, as mutations in a conserved basic domain in SMARCB1 (Snf5 homolog) disrupt binding to the nucleosome, reduce remodeling rates, and have defects in cell-type differentiation 40 .…”

“…Fig. 5) [20][21][22][23][24] . The C-terminal end of the HSA helix contacts the ATPase and engages with the post-HSA and P1 domains, as well as the Brace Helices ( Fig.…”

“…Removal of the ARPs from the full RSC complex results in basal remodelling roughly equivalent to that of Sth1 alone, suggesting that they perform a core function in activating remodeling by RSC 18 . A mechanistic understanding of these regulatory interactions is still missing as the recent cryo-EM structures of the yeast RSC [20][21][22] and SWI/SNF 23 complexes, and the BAF complex, the human ortholog of SWI/SNF 24 did not reach high enough resolution in the ARP module or the HSA/post-HSA/P1 regulatory hub. To bridge this gap, we focused on the well-characterized Sth1/Arp7/Arp9/Rtt102 RSC sub-complex ( Fig.1a) that has been used to gain much of our current understanding of the regulation of remodeling in RSC 17,18,[25][26][27] .…”