Fig. 3

Evaluate the impact of global RNA depletion on CTCF’s DNA binding affinity by CTCF ChIP-seq. A Schematic diagram illustrating how the CTCF-ChIP-seq works in combination with triptolide and RNase A treatment. B Summary of differential CTCF-binding peaks by paired analysis. Up and down peaks were defined by comparing triptolide vs DMSO and +/− RNase A groups at cutoffs with different stringencies; high stringent cutoff: fold change FC > 2 and FDR < 0.05; modest stringent cutoff: FC > 2 and P < 0.05. Overlapped peaks between different comparisons were connected by the solid line. C Motif analysis of 313 differential CTCF-binding peaks collected from RNase A treatment vs no treatment. The top 5 were shown according to Homer known motif analysis. D Motif analysis of differential CTCF-binding peaks collected from triptolide treatment vs DMSO treatment with the cutoff of FC > 2 and P < 0.05. The top 5 were shown according to Homer known motif analysis. E Genomic distribution of differential CTCF-binding peaks collected from RNase A treatment vs no treatment. With the cutoff of FC > 2 and FDR < 0.05, about 313 peaks were identified and assigned to different genomic regions. F Genomic distribution of total CTCF-binding peaks (38,728)