Fig. 2

Human Nanog locus forms a chromatin loop between x45s and x14s Alus upon cell differentiation in NTERA cell line. a Chromosome conformation capture (3C) assay using coordinates 3 and 6 as hooks. The relative crosslinking frequency was quantified in NTERA-wt cells untreated (UT, blue), treated with RA for 48 h (red) and in NTERA-sh cells UT (green), RA for 48 h (black). 3 + X (left) and 6 + X (right) primer combinations were addressed. b Chromosome conformation capture (3C) assay using coordinate 3 as hook. The relative crosslinking frequency was quantified in NTERA-wt cells untreated (UT, blue), treated with RA for 48 h (red) and in NTERA-CRISPRx45s cells UT (green), RA for 48 h (black). 3 + X primers combinations were addressed. c 3C assay using coordinate 6 as hook. The relative crosslinking frequency was quantified in NTERA-wt cells untreated (UT, blue), treated with RA for 48 h (red) and in NTERA-CRISPRx45s cells UT (green), RA for 48 h (black). 6 + X primers combinations were addressed. Three biological replicates and two experimental replicates were done for a. Two biological replicates and two experimental replicates were done for b and c. *P < 0.05, **P < 0.01 and ***P < 0.001. Data are shown as mean ± SD