Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome

Abstract

Chromatin remodelling complexes of the SWI/SNF family function in the formation of nucleosome-depleted, transcriptionally active promoter regions (NDRs) 1 , 2 . The essential Saccharomyces cerevisiae SWI/SNF complex RSC 3 contains 16 subunits, including the ATP-dependent DNA translocase Sth1 4 , 5 . RSC removes nucleosomes from promoter regions 6 , 7 and positions the specialized +1 and –1 nucleosomes that flank NDRs 8 , 9 . Here, we present the cryo-EM structure of RSC in complex with a nucleosome substrate. The structure reveals that RSC forms five protein modules and suggests key features of the remodelling mechanism. The body module serves as a scaffold for the four flexible modules that we call DNA-interacting, ATPase, arm and ARP modules. The DNA-interacting module binds extra-nucleosomal DNA and is involved in the recognition of promoter DNA elements 8 , 10 , 11 that influence RSC functionality 12 . The ATPase and arm modules sandwich the nucleosome disc with their ‘SnAC’ and ‘finger’ elements, respectively. The translocase motor of the ATPase module engages with the edge of the nucleosome at superhelical location +2. The mobile ARP module may modulate translocase-nucleosome interactions to regulate RSC activity 5 . The RSC-nucleosome structure provides a basis for understanding NDR formation and the structure and function of human SWI/SNF complexes that are frequently mutated in cancer 13 .

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

“…8a,b). This Sth1 density seems to directly interact with a region of the nucleosome known as the acidic patch, in agreement with a similar density observed in cryo-EM reconstructions of the full RSC complex 21 . The nucleosome acidic patch is composed of 8 acidic residues found on histones H2A and H2B and is used by many proteins to interact with the nucleosome [32][33][34][35] (Fig.…”

“…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] .…”