Fig. 4: SMARCA4 missense mutants are deficient in opening chromatin and inducing gene expression.

a FRET nucleosome remodeling assays were performed with immunopurified SMARCA4 WT and mutants from 293T cells transduced with SMARCA4 WT or mutants. Cy3/Cy5 ratios are represented in a 60 min kinetic assay, each construct is normalized to its no ATP control (n = 2 biologically independent samples, lines represent the mean). b Significantly open and closed sites as measured by ATAC-seq in NCI-H1944 cells expressing SMARCA4 WT or mutants relative to the LACZ control (n = 2 per construct). Significance was tested with a moderated t-statistic (two-sided) and P values were adjusted for multiple testing with the Benjamini–Hochberg procedure. c Heatmap of ATAC-seq changes relative to LACZ control (log₂ fold-change) in the union of sites opened and closed from b (n = 2 per construct). d Representative IGV track of SMARCA2/SMARCA4 ChIP-seq and ATAC-seq changes in cells from b (overlay of 2 replicates per construct). e Heatmap of chromatin accessibility and SMARCA2 and SMARCA4 occupancy at sites from c in NCI-H1944 cells transduced with the LACZ control or SMARCA4 WT (n = 2 per construct). Data are shown as normalized peak counts per million genomic DNA fragments in a 2 kb window around the peak center. Rows are rank ordered by ATAC-seq peaks. R, replicate. f Heatmap of qRT-PCR analysis of a subset of SMARCA4 WT-induced genes in NCI-H1944 cells transduced with SMARCA4 WT or mutants (mean of n = 3 biologically independent samples). g SMARCA4 qChIP at target genes and a negative control region on chr14 in cells from f (each dot represents a technical replicate, n = 2; representative of 3 independent experiments). Source data are provided as a Source Data file.