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. Author manuscript; available in PMC: 2022 Oct 20.
Published in final edited form as: Nat Struct Mol Biol. 2022 Sep 12;29(9):891–897. doi: 10.1038/s41594-022-00821-8

Figure 3. Depletion of cohesin, but not of CTCF, inhibits distal enhancer driven gene activation.

Figure 3

(a) Timecourse of TALE transfection and auxin treatment is shown above. Percentage of (left axis) Shh and (right axis) Lmbr1 expressing alleles, assayed by RNA FISH, in TALE-transfected CTCF-AID cells either untreated (- auxin) or treated with 24 hours of auxin (+ auxin). Cells were transfected with tShh-VP64, tSBE2-VP64 and tZRS-VP64 and equivalent TALE-Δ controls. Data shown are from one biological replicate. Data from an independent biological replicate are shown in Extended Data Fig. 3a. The data were compared using a two-sided Fisher’s Exact Test, n = numer of alleles scored, ns – not significant (p>0.05). Source data Fig3. (b) Images from representative nuclei from - & + auxin CTCF-AID cells showing DNA FISH signals for Shh/SBE2/ZRS probes. Scale bars: 5 μm. (c) Violin plots showing the distribution of interprobe distances (μm) between Shh/SBE2, SBE2/ZRS, Shh/ZRS probes in tSBE2-Vp64- and tZRS-Vp64-transfected CTCF-AID cells - & + auxin. *p<0.05, **p<0.01, ****p<0.0001 (two-sided Mann-Whitney U-tests). Values for number of alleles scored, mean and inter-quartile distances are in Extended Data Fig 3e. d) As for (a) but for SCC1-AID with 6 hours of auxin (+ auxin). Source data Fig3. Biological replicate for those data in Extended Data Fig 3b. ns p>0.05 *p<0.05 **p<0.01 (Fisher’s Exact tests). (e) and (f) As for (b) and (c) but for SCC1-AID cells.