Fig. 2 |. Characterization of chromatin CTCF/Rad21-binding and transcription across the V_H locus in G1-arrested parental and IAA-treated CTCF-degron cells.

a, Schematic of the entire murine Igh locus with details as shown in Fig. 1a. b, The four V_H domains are highlighted different colors which are maintained in related figures. c-e, Average signal counts ± s.e.m. of CTCF (c) and Rad21 (d) ChIP-seq and GRO-seq (e) from three biologically independent experiments across the four highlighted V_H domains in G1-arrested parental and IAA-treated CTCF-degron cells are plotted. S/AS: sense/anti-sense transcription. See Extended Data Fig. 4a,b and 5a for the plots across other parts of Igh locus. V_Hs for comparisons in Fig. 3 are highlighted. f-i, Box-and-Whisker plots are presented with median, upper and lower quartiles and whiskers showing 1.5x interquartile range for CTCF (f) and Rad21 (g) ChIP-seq, GRO-seq (h), and 3C-HTGTS (i) signal counts within indicated V_H domains in G1-arrested parental (“Par.”) and IAA-treated CTCF-degron cells. n=3 biological repeats with similar results for each condition in f-i. p values were calculated using two-sided Mann-Whitney U test. See Methods for details. Comparison of panels (f) and (h) reveals that residual CTCF binding levels are significantly higher in the highly transcribed distal V_H domain than those of the proximal domains with less overall transcription, which might reflect known roles of transcription in CTCF chromatin binding^33,34.