Mechanism and Regulation of the SWI/SNF Family of ATP‐dependent Chromatin Remodelers

In yeast there are two SWI/SNF complexes and in mammals there is a family of an estimated ~100 complexes, each with different combinations of related subunits. Efforts in sequencing many cancer genomes has revealed that mammalian SWI/SNF complexes is one of the most frequently mutated epigenetic factors found in a broad range of cancers. In order to understand more about the subunit organization of SWI/SNF and because yeast and mammalian SWI/SNF complexes share many conserved subunits and domains; we have mapped the inter‐subunit and intra‐subunit interactions of the yeast SWI/SNF complex with lysine specific homo bi‐functional crosslinkers and mass spectrometry. The A‐T motif was shown to extensively interact with the ATPase domain, and is well conserved throughout all eukaryotes and targeted in colorectal and endometrial cancers. Deletion of the A‐T hook in yeast SWI/SNF reduced the DNA‐stimulated ATPase and consequently the nucleosome mobilizing activities of the complex without affecting the subunit composition or nucleosome binding affinity. Loss of the A‐T hook effects only a small subset of the genes regulated by SWI/SNF as shown by RNA‐seq analysis and suggests that mutation of the A‐T hook creates an aberrant form of SWI/SNF that impacts a subset of its target genes. Further analysis using MNase‐seq has found that in the absence of the A‐T hook domain the occupancy of the +1 nucleosome, immediately downstream of the transcription start site, is decreased and implicates a role of SWI/SNF in helping to assemble or maintain nucleosomes at this position. The A‐T hook of murine Brg1 was deleted in embryonic stem cells using CRISPR‐Cas9 and the role of the A‐T hook in mammalian SWI/SNF analyzed by RNA‐seq and ChIP‐seq as will be discussed in more detail. In addition the Snf5 subunit of yeast SWI/SNF was found to interact with the ATPase domain of the catalytic subunit. When the Snf5 subunit was deleted several other subunits were also lost from the complex and formed an aberrant version of the SWI/SNF complex due to changes in subunit composition. We have carefully mapped the changes in nucleosomal interactions and nucleosome mobilizing activities that occur with the loss of the SNF5 sub‐module. The Snf5 subunit is required for the stable interactions of the catalytic subunit with nucleosomal DNA in the absence of ATP. The mammalian ortholog of SNF5 or SMARCB1 is a tumor suppressor gene and the loss of this subunit is a driver mutation in pediatric rhabdoid sarcomas. Our data suggest how the loss of SNF5 might alter the activity of SWI/SNF, which in turn could lead to oncogenesis. Support or Funding Information NIH grant GM 48413