Extended Data Fig. 3: CTCF depletion does not impair transdifferentiation or long-range enhancer-promoter contact dynamics.

a, Representative flow cytometry analysis of CD19 and Mac-1 marker expression during transdifferentiation of CTCF-mAID B cells treated with DMSO or auxin. The experiment was repeated 3 times with similar results. b, Transdifferentiation kinetics of CTCF-mAID B cells (clone C1) in the presence of DMSO or auxin analysed at 0, 96 and 168 hpi by flow cytometry for CD19 and Mac-1 expression (n = 3 biologically independent samples). Centre indicates mean, error bars show standard deviation and P unpaired two-tailed t-test. c, Phagocytosis assay of iMacs analyzed by flow cytometry showing uptake of blue fluorescent beads. The experiment was repeated 3 times with similar results. d, RNA expression measured by qRT-PCR of cytokines in noninduced (NI) or 2h LPS-induced iMacs DMSO (n = 6), iMacs AUX (n = 6) or B cells (n = 3). Mean values are shown, error bars represent standard error and n represents biologically independent samples. e, Venn diagram showing the overlap of genes upregulated (left) and downregulated (right) in iMacs after transdifferentiation in the presence of DMSO or auxin based on RNA-Seq (n = 2 biologically independent samples). f, Gene ontology analysis of genes specifically upregulated (n = 419) and downregulated (n = 744) specifically in CTCF-depleted iMacs (q-value, FDR corrected Fisher exact test). g, Aggregate metaplots (10-kb resolution) depicting long range (5–10-Mb) interaction frequencies between enhancers and promoter (E-P) during transdifferentiation. Area shown is centered on enhancers or promoters ± 250-kb). h, Venn diagram showing the number of switching compartment regions (100-kb bins) during transdifferentiation in presence of DMSO or auxin. i, Expression of MAFB during transdifferentiation with or without CTCF, as measured by RNA-seq (n = 2 biologically independent samples, lines connect mean values). j, Enhancer activity at the MAFB locus during transdifferentiation. Browser snapshot showing H3K27ac ChIP-seq profiles of a 4-Mb domain surrounding the MAFB locus. The enhancer and the promoter shown in Fig. 3g are highlighted in light brown.