Fig 2: Model: Dual tumor-suppressor activities of SNF5. a In the absence of SNF5, MYC binds unimpeded to chromatin to promote gene expression programs that maintain the MRT state. Under these conditions, transcription start site (TSS)-distal sites that regulate transcription of genes involved in development and differentiation remain in a closed state, repressing transcription. b When SNF5 is present, MYC binding to DNA is tempered and RNA polymerase pauses at these genes, repressing transcription. SNF5, in concert with the SWI/SNF complex (gray), also leads to remodeling at TSS-distal sites, resulting in an open chromatin state and activation of genes linked to development and differentiation

Fig 3: Low SNF5 expression confers poor outcomes in BC patients. A The Kaplan–Meier analysis of overall survival in TCGA database and B GSE13507 cohort. ROC curves for C TCGA and D GSE13507 cohorts

Fig 4: CREB1 and BAF47 are essential for transcriptional activation of Neo-1 in endothelial cells. (A) Neo-1 promoter-luciferase constructs were transfected into EAhy926 cells followed by treatment with oxLDL (50 μg/ml) for 24 h. Luciferase activities were normalized by protein concentration and GFP fluorescence. (B) Ingenuity pathway analysis. (C) EAhy926 cells were transfected with indicated siRNAs. Knockdown efficiencies were examined by Western. (D,E) EAhy926 cells and HAECs were transfected with indicated siRNAs followed by treatment with oxLDL (50 μg/ml) for 24 h. Neo-1 expression was examined by qPCR and Western. (F) EAhy926 cells and HAECs were treated with oxLDL (50 μg/ml) and harvested at indicated time points. ChIP assays were performed with anti-CREB1, anti-BAF47, or IgG.

Fig 5: SNF5 inhibits chromatin binding by MYC in MRT cells. a Known motif enrichment analysis was performed on the ChIP-Seq data from G401 cells expressing EGFP. The top four motifs are shown; all are enriched in the E-box sequence (CACGTG). b MYC peaks in the EGFP-expressing cells were quantified in terms of their distance to the nearest annotated transcriptional start-site (TSS). Peaks within 1 kb of a TSS are called as “promoter” peaks. c MYC peaks located within 1 kb from a TSS were assigned to their nearest gene and GO term enrichment analysis was performed. d Overlap of MYC peaks obtained from EGFP-expressing G401 cells with six published MYC ChIP-seq data sets: NB4 acute promyelocytic leukemia cells (GSM935643), hESC human embryonic stem cells (GSM935509), Ramos Burkitt’s lymphoma cells (GSM762711), A549 lung cancer cells (GSM1003607), K562 chronic myeloid leukemia cells (GSM935516), and MCF7 breast cancer cells (GSM1006866). e MYC peaks that are located within 1 kb from a TSS were assigned to their nearest gene and overlaid with two MSigDB Hallmark MYC target data sets. A hypergeometric test was performed; significance is displayed below the Venn diagram. f Scatterplot of normalized peak read counts for each condition (average of replicates), ranked based on EGFP peak read number. g Heat maps of MYC peak intensity for each condition representing the combined average of normalized peak intensity in 100-bp bins ± 2 kb around the center of peaks. Genes ranked based on EGFP. h Two example genome browser tracks from each condition. i Box-and-whisker plot of log2-fold changes of MYC peaks for OMOMYC or SNF5 samples (FDR < 0.05), relative to EGFP. Box extends from 25th to 75th percentile with median marked by the middle line, whiskers extend from minimum to maximum point. n = 2 independent ChIP-seq experiments