Fig. 6

Multi-omics integration reveals main CTCF co-regulatory partners in regulating downstream gene expression. A Scheme of multi-omics analyses including CRISPR dropout screening, ATAC-seq, RNA-seq, proteomics, and phosphoproteomics with total 1639 TFs, 132,266 DARs, 11,119 mRNAs, 10,317 proteins, and 11,924 phosphopeptides respectively. B Summary of DE analysis for each dataset. C More DE proteins were identified compared to DE mRNAs upon CTCF acute loss. The scatterplot shows the log₂ fold change of proteins (x-axis) and log₂ fold change of mRNAs (y-axis) upon CTCF acute loss at 24 h. Pearson correlation coefficient and representative gene names are labeled. D CTCF co-regulatory TFs revealed by multi-omics integration. Heatmaps indicate (1) the enrichment (FDR) of downstream DE genes of CTCF partner TFs at RNA and protein levels showing either upregulation or downregulation (red). (2) FDR values of the DE analyses comparing the expression of these TFs in acute CTCF loss groups to the control group in the transcriptome, proteome, and phosphoproteome data (purple). (3) Enrichment (Log₂ OddRatio) of TFs at decreased DAR and increased DAR (blue). (4) Survival essential genes identified in the CRISPR-Cas9 dropout screening in SEM cells (asterisk). E The physical distance between CTCF and ZBTB7A binding motifs was calculated within increased, decreased, and control DARs, normalized to peak size. F The physical distance between CTCF and YY1 binding motifs was calculated within increased, decreased, and control DARs, normalized to peak size. G The physical distance between CTCF and negative control DUX4 binding motifs was calculated within increased, decreased, and control DARs, which were normalized to peak size. Student’s t test