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Fig. 5 | Clinical Epigenetics

Fig. 5

From: Hi-C profiling of cancer spheroids identifies 3D-growth-specific chromatin interactions in breast cancer endocrine resistance

Fig. 5

Conducting 3C/RT-qPCR and 3D-FISH validations of differentially expressed looping genes in 3D spheroids of BC cells. A 3C-qPCR showing enhanced interaction frequencies of each gene loop for ZDHHC7, TEAD3, PRKD3, LATS2 and MET in MCF7TR_3D compared to those in MCF7_3D. Three biological replicates were performed for each gene loop with a statistical significance (***p ≤ 0.01; **p ≤ 0.05) by one-tail paired t test analysis. Error bars represent standard deviation with three experiments. B RT-qPCR showing increased gene expression levels of ZDHHC7, TEAD3, PRKD3, LATS2 and RASSF3 in MCF7TR_3D compared to those in MCF7_3D. Three biological replicates were performed for each gene loop with a statistical significance (***p ≤ 0.01; **p ≤ 0.05; *p ≤ 0.1) by one-tail paired t test analysis. Error bars represent standard deviation with three experiments. C 3D-FISH images showing interaction frequency of the PRKD3 loop in MCF7TR_3D and MCF7_3D, respectively. BAC probe combinations: promoter (green) and distal region (red) n = 50, DAPI DNA stain (blue). Square boxes in red represent the magnified view of each interaction. Scale bar at 5 µm. D Distributions of measured distances of the PRKD3 loop are significantly different for MCF7TR_3D vs. MCF7_3D (*p ≤ 0.1) by one-tail paired t test analysis. Distances were measured between the closest two foci in each nucleus

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