Background: BAF chromatin remodeling complexes are multi-protein molecular machines that remodel chromatin architecture to regulate gene expression, however the subunit-specific mechanisms by which this activity is achieved remain incompletely defined. SMARCB1 (BAF47) is a core subunit of BAF complexes, and recent genetic sequencing studies have revealed an accumulation of single amino acid mutations in the highly conserved, yet functionally uncharacterized C-terminal domain (CTD) of SMARCB1, which cause the intellectual disability disorder, Coffin-Siris syndrome (CSS), and are present in a variety of cancers.

 

Hypothesis & Research Methods: Given its conservation through yeast, I hypothesized that these disease-associated mutations disrupt the fundamental, nucleosome remodeling activity of BAF complexes. In order to assess my hypothesis, I used a variety of biochemical (peptide pull-down and chromatin remodeling assays), structural (3D-protein NMR), and chromatin mapping (ChIP-seq and ATAC-seq) experiments to define the molecular and genome-wide regulatory consequences of recurrent single-residue mutations in the SMARCB1-CTD, implicated in CSS and cancer.

 

Findings and Significance: Intriguingly, through peptide pull-down assays I discovered that the SMARCB1-CTD directly binds nucleosomes and that all CSS-associated mutations disrupt this interaction. Furthermore, 3D-structural determination of this region through protein NMR revealed an alpha helix structure with a positively charged cluster of amino acids, all mutated in CSS. Lastly, single amino acid SMARCB1-CTD mutations significantly abrogate mSWI/SNF complex-mediated chromatin remodeling activity in vitro and DNA accessibility in human cells (by ATAC-seq), without changes in genome-wide complex localization (by ChIP-seq).

 

Big Picture: Taken together, these studies provide the first molecular mechanism of the intellectual disability disorder CSS, and unmask a major, evolutionarily conserved function of SMARCB1 that dates back over 900 million years.