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. Author manuscript; available in PMC: 2020 May 2.
Published in final edited form as: Mol Cell. 2019 Sep 12;76(3):412–422.e5. doi: 10.1016/j.molcel.2019.08.015

Figure 2. Deletions in ZF1 and ZF10 Independently Abolish CTCF Binding to RNA.

Figure 2.

(A) Schematic representation of known domains of WT CTCF with its 11 zinc fingers being numbered (top); smoothed residue-level RBR-ID score (He et al., 2016), plotted along the primary sequence (bottom).

(B) FACS analysis highlighting percentage of GFP+ or mCherry+ CTCF-AID-GFP mESCs with or without rescue of CTCF: WT, ZF1Δ, or ZF10Δ.

(C) Immunoprecipitation of all rescue cell lines indicated and immunoblots for CTCF and Rad21.

(D) Representative image of GFP-CTCF incubated with each rescue, immunoprecipitated with a GFP antibody and blotted against CTCF (left); bar graph quantification of each rescue protein relative to the GFP-CTCF (n = 5) (right).

(E) PAR-CLIP of stably expressed WT and mutant CTCF in mESCs. Autoradiography for 32P-labeled RNA (top) and control western blot (middle and bottom).

(F) Schematic representation of ZF1 and ZF10 of CTCF; mutations found in breast and endometrial cancer that alter zinc binding are shown in black; mutations that do not alter zinc binding are in blue, and RBR-ID deletions are in brackets.