Cryo-EM structure of SWI/SNF chromatin remodeling complex with nucleosome

Abstract

The chromatin remodeling complex SWI/SNF is highly conserved and plays critical roles in various cellular processes including transcription and DNA damage repair ^{1, 2} . It hydrolyzes ATP to remodel chromatin structure by sliding and evicting histone octamers ^{3- 8} , creating DNA regions that become accessible to other essential factors. However, our mechanistic understanding of the remodeling activity is largely hindered by the lack of a high-resolution structure of any complex from this family. Here we report the first structure of SWI/SNF from the yeast S. cerevisiae bound to a nucleosome at near atomic resolution determined by cryo-electron microscopy (cryo-EM). In the structure, the Arp module is sandwiched between the ATPase and the rest of the complex, with the Snf2 HSA domain connecting all modules. The body contains an assembly scaffold composed of conserved subunits Snf12 (SMARCD/BAF60), Snf5 (SMARCB1/BAF47/ INI1) and an asymmetric dimer of Swi3 (SMARCC/BAF155/170). Another conserved subunit Swi1 (ARID1/BAF250) resides in the core of SWI/SNF, acting as a molecular hub. We also observed interactions between Snf5 and the histones at the acidic patch, which could serve as an anchor during active DNA translocation. Our structure allows us to map and rationalize a subset of cancer-related mutations in the human SWI/SNF complex and propose a model of how SWI/SNF recognizes and remodels the +1 nucleosome to generate nucleosome-depleted regions during gene activation ⁹ .