Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes

Abstract

SUMMARY Mammalian SWI/SNF (mSWI/SNF) ATP-dependent chromatin remodeling complexes are multi-subunit molecular machines that play vital roles in regulating genomic architecture and are frequently disrupted in human cancer and developmental disorders. To date, the modular organization and pathways of assembly of these chromatin regulators remain unknown, presenting a major barrier to structural and functional determination. Here, we elucidate the architecture and assembly pathway across three classes of mSWI/SNF complexes—canonical BRGI/BRM-associated factor (BAF), polybromo-associated BAF (PBAF), and newly defined ncBAF complexes—and define the requirement of each subunit for complex formation and stability. Using affinity purification of endogenous complexes from mammalian and Drosophila cells coupled with cross-linking mass spectrometry (CX-MS) and mutagenesis, we uncover three distinct and evolutionarily conserved modules, their organization, and the temporal incorporation of these modules into each complete mSWI/SNF complex class. Finally, we map human disease-associated mutations within subunits and modules, defining specific topological regions that are affected upon subunit perturbation.

Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement

“…We used the ~250 ug RSC2 TAP-tag purified RSC complex and crosslinked by 4mM bis(sulfosuccinimidyl)suberate (BS3) at RT for 2 hours. Sample processing and mass spectrometry data analyses were done as described before 16 . After plink2 and Nexus database searches against the RSC subunit sequences, about 6.6% of interlinked spectra and 3.1% intralinked spectra were removed after manually spectrum checking.…”

“…It is important to note that this initial assembly process only involves evolutionarily conserved subunits and thus is likely conserved for all SWI/SNF chromatin remodelers ( Fig. S5a) 15,16 . This conclusion is further supported by the structural similarities we observe between the yeast SWI-SNF and RSC complexes, and by the previous mass spectrometry analysis of the assembly of human BAF complexes 16 .…”

Xmas ESC: A new female embryonic stem cell system that reveals the BAF complex as a key regulator of the establishment of X chromosome inactivation

“…Our screen revealed a role for Smarcc1 and Smarca4 in the establishment of XCI. Both Smarcc1 (also known as Baf155) and Smarca4 (also known as Brg1) are members of the chromatin remodelling BAF (SWI/SNF) complex, with Smarcc1 being the core subunit around which the complex forms (Mashtalir et al, 2018) and Smarca4 being one of a variable number of catalytic ATPase subunits (Wang et al, 1996a;Wang et al, 1996b). Interestingly, the BAF complex is made up of different subunits dependent on cell type, with both Smarcc1 and Smarca4 being part of a ESC-specific complex (known as esBAF), required for both pluripotency and self-renewal (Fazzio et al, 2008;Ho et al, 2009;Kaeser et al, 2008).…”

Synthetic lethal therapy based on targeting the vulnerability of SWI/SNF chromatin remodeling complex‐deficient cancers

“…Mutations in SWI/SNF chromatin remodeling genes occur with high frequency in cancer; they are detected in approximately 20% of all cancer patients . The SWI/SNF chromatin remodeling complex is composed of 15 subunits, and it is classified into 3 complexes comprising different subunits (Figure ): the BRG1/BRM‐associated factor (BAF) complex, the polybromo‐associated BAF (PBAF) complex, and the noncanonical BAF (ncBAF) complex . The function of the SWI/SNF chromatin remodeling complex relies on the catalytic activities of the SWI/SNF2‐like ATPase and helicase domains.…”