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. Author manuscript; available in PMC: 2020 Sep 19.
Published in final edited form as: Mol Cell. 2019 Jul 31;75(6):1229–1242.e5. doi: 10.1016/j.molcel.2019.06.025

Figure 5: Extent of local chromatin interactions does not depend on locus accessibility and CTCF binding at the extended Ifng/Ifng-as1 loci.

Figure 5:

(A)(B) Looping interactions within the Ifng/Ifng-as1 loci were analyzed by 3C between the +66 kb (66 kb downstream of Ifng TSS) HindIII fragment as anchor (shown in violet) and different fragments positioned at increasing distances from the anchor. Shown are representative data from n=3 independent experiments using Th1 cells (A) or Th2 cells (B). Dashed lines indicate deleted DNA fragment in Ifng-as1 KO cells. (C) ATAC sequencing profiles comparing WT and Ifng-as1 KO Th1 and Th2 cells. Shown are representative tracks from n=2 independent experiments (D) ATAC sequencing profiles for WT and Ifng-as1-PolyA KI Th1 and Th2 cells. Shown are representative tracks from n=2 independent experiments. 26 ATAC peaks (indicated in red) were called in a 340 kb region encompassing Ifng and Ifng-as1. (E) Statistical significance (p-values) of peak calling between WT and Ifng-as1-PolyA KI Th1 ATAC sequencing samples (F) Genomic tracks of CTCF binding comparing Th1 and Th2 cells (day 6 of culture) isolated from WT and Ifng-as1 KO mice and Ifng-as1-PolyA KI mice. Shown are representative tracks from n=2 independent experiments. See also Table T1.