Fig. 4

Interrogate CTCF target genes based on multi-omics integrative analysis. a The number of TADs called from CTCF-AID HEL cells is shown with or without 24 h of IAA treatment. The reproducibility of the Hi-C data from two independent replicates was high, allowing the integration of raw Hi-C data to recall TADs. b The number of chromatin loops called from CTCF-AID HEL cells is shown with or without 24 h of IAA treatment. The reproducibility of the Hi-C data from two independent replicates was high, allowing the integration of raw Hi-C data to recall loops. c Violin plot showing the relative fold change in normalized contact numbers from Hi-C in CTCF-AID HEL cells (+ IAA versus − IAA) at loops grouped by whether the loop anchors overlapped the DARs from ATAC-seq (left panel) or the DEGs from RNA-seq relative to their corresponding control groups. *** P < 0.001; **** P < 0.0001, according to the Wilcoxon test. d Screenshot of the metabolism-related gene example FXN, with ATAC-seq, CTCF ChIP-seq, and GATA1 ChIP-seq signals and annotated TAD domains and chromatin loops from the genome-wide Hi-C interaction map before and after IAA treatment in CTCF-AID HEL cells. The red arrow highlights the decreased ATAC-seq and CTCF ChIP-seq peaks in the enhancer and promoter regions. The black cycle indicates the position of loops identified with lost contacts after IAA treatment in CTCF-AID HEL cells. e Screenshot of the metabolism-related gene example GOT2, with ATAC-seq, CTCF ChIP-seq, and GATA1 ChIP-seq signals and annotated TAD domains and chromatin loops from the genome-wide Hi-C interaction map before and after IAA treatment in CTCF-AID HEL cells. The red arrow highlights the decreased ATAC-seq and CTCF ChIP-seq peaks in the promoter region. The black cycle indicates the loop position identified with lost contacts after IAA treatment in CTCF-AID HEL cells. f In both the immature and mature states, the validated mRNA level of FXN expression in the CTCF-AID HUDEP-2 and HEL cells was obtained without and with IAA treatment. The mRNA level was determined relative to that of β-actin from three replicates. ** P < 0.01, *** P < 0.001, **** P < 0.0001, unpaired Student’s t test. g In both the immature and mature states, the validated mRNA level of GOT2 expression in the CTCF-AID HUDEP-2 cells and HEL cells without and with IAA treatment. The mRNA level was determined relative to that of β-actin from three replicates. ** P < 0.01; *** P < 0.001, **** P < 0.0001, unpaired Student’s t test