Fig. 3: Knockdown of SWI/SNF-bound lncRNAs causes a global genomic redistribution of SWI/SNF.
From: Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers
a BRG1 CUT&RUN lost (blue) and gained (red) peaks following lncRNA knockdowns. Negative control siRNA (siCTL) compared to untransfected control (top left). siRNA lncRNA knockdowns compared to siCTL. b ChromHMM chromatin state analysis of BRG1 binding patterns after lncRNA knockdown. c–f Visualization of specific lncRNA knockdowns illustrating BRG1 binding changes. Example traces for MIR100HG (c), JPX (d), and PVT1 (e) knockdowns highlight reduced BRG1 binding at enhancers (indicated by purple rectangles), while increased BRG1 binding at enhancers is observed in LINC00342 knockdown (f). g Browser traces of BRG1 CUT&RUN after siRNA-mediated knockdown of MIR100HG and knockdown followed by overexpression rescue with a MIR100HG transcript. 5 different genomic regions annotated with ChromHMM are shown. siRNA control (siCTL). h Browser traces of BRG1 CUT&RUN after siRNA-mediated knockdown of JPX and knockdown followed by overexpression rescue with a JPX transcript. 5 different genomic regions annotated with ChromHMM are shown. siRNA control (siCTL). Source data are provided as a Source Data file.
