Fig. 4: LncRNAs retain BRG1 at functional SWI/SNF-dependent enhancers.
From: Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers
a Volcano plots of differential ATAC-seq peaks after treatment with a PROTAC against BRG1 and BRM ATPases. 30, 60 and 240 minutes of PROTAC treatment are displayed. b BRG1 binding (CUT&RUN) and corresponding chromatin accessibility (ATAC-seq) at enhancers and promoters after PROTAC treatment. c Upset plot of total lost enhancers for each lncRNA knockdown and their overlap. d Enhancers lost with any lncRNA siRNA, PROTAC and both. e Number of DEG (Differentially Expressed Gene) promoters associated with enhancers perturbed by both siRNA of lncRNAs and PROTAC. f Number of DEGs after PROTAC that loop to enhancers lost after siRNA knockdown of individual lncRNAs. g Number of BRG1-dependent enhancers lost after LINC00607 CRISPR knockout (KO), overlapped with the differential expression (DE) of the connected genes after LINC00607 siRNA. h Browser visualization of an enhancer (right-most) sensitive to PROTAC (lost BRG1 CUT&RUN binding and diminished ATAC peak) and siRNA against LINC00607. P-E loops (Promoter-Enhancer loops). Source data are provided as a Source Data file.
