Fig. 4
From: Deciphering the role of RNA in regulating CTCF’s DNA binding affinity in leukemia cells
CTCF’s RNA binding domain deficiency or global RNA depletion does not impact genome-wide chromatin accessibility. A Genomic heatmap of ATAC-seq signals matched to reproducible CTCF peaks from CTCFAID2/WT cells and CTCFAID2/dRBR. ATAC-seq tracks from CTCFAID2 with or without auxin (5-Ph-IAA) treatment were shown as controls. B Spearman’s correlation of all ATAC-seq signals defined by A was calculated to quantify the similarity between samples. C ATAC-seq tracks from CTCF-WT and CTCF-dRBR at the MYC locus show consistent chromatin accessibility patterns across all samples. CTCFAID2 with or without auxin (5-Ph-IAA) treatment were shown as controls. D ATAC-seq tracks from CTCF-WT and CTCF-dRBR at the RBM45 locus show consistent chromatin accessibility patterns across all samples. CTCFAID2 with or without auxin (5-Ph-IAA) treatment were shown as controls. E Total RNA-seq was performed to quantify the global gene expression changes between CTCF-dRBR and CTCF-WT groups based on the cutoff of FDR < 0.05. N = 3. F The mRNA expression of CTCF target genes RBM45 and MYC between CTCF-dRBR and CTCF-WT groups. n.s., no statistic difference, calculated by unpaired t-test. N = 3