Figure 2.

Functional role of Dref in 3D chromatin organization of BG3 cells. (A) Classification of robust TAD borders as described in the main text: lost (borders that are strong in WT and completely disappear in the knockdown); maintained (borders that are strong in WT and are maintained strong in the knockdown); and new (borders that appear strong in the knockdown); see Supplemental Figure S3A. (B) Overlap of lost, maintained, and new borders in the three knockdowns. (C) Number and percentage of maintained, lost, and new borders that have direct binding of BEAF-32, Cp190, and/or Chro (see Supplemental Fig. S4B). We considered common borders between the all three knockdowns (BEAF-32 single knockdown, Cp190 and Chro double knockdown, and BEAF-32 and Dref double knockdown). (D) Examples of genomic regions at DpnII restriction size resolution for BEAF-32 Dref double knockdown. We used the same types of plots as in Figure 1E,F.