Extended Data Fig. 2: ISWI accessory subunit deletions are subcomplex-specific, and their transcriptional response shows a similarity between loss of BPTF and loss of SNF2H.
From: Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF
a. SNF2H co-immunoprecipitations followed by western blot against ISWI subunits in WT and ISWI deletion lines as indicated. Blots for detection of BPTF and SNF2H are representative of at least two experiments. Blots for the detection of all other proteins have not been repeated. b. Expression of several pluripotency markers (log2 RPKM) in WT and ISWI deletion lines. c. RNA changes in the generated deletion lines are shown as MA plots. Differentially expressed genes are shown as blue (downregulated) and red (upregulated) dots. d. Quantitative comparison of RNA changes (log2FC) upon deletion of accessory subunits (x-axis) versus SNF2H deletion (y-axis). R: Pearson’s correlation coefficient. e. Heatmap of Pearson’s correlation of transcriptional changes induced by each deletion. Correlation was calculated on log2 fold change data of genes called as differentially expressed in at least one contrast. f. Principal component analysis of transcriptional changes induced by each ISWI deletion. PCA was performed on log2 fold change data of genes called as differentially expressed in at least one contrast.
