Fig. 3

Localization and molecular characteristic of TGFB2 PIRs within the TGFB2 TAD. A Localization of the TGFB2 PIRs within the TGFB2 TAD. The NG Capture-C data obtained by Bejjani et al. [36] in MDA-MB-231 cells (lower panel) were aligned with the Hi-C contact matrix established by Rao et al. [55] in primary human mammary epithelial cells (HMECs) (upper panel). Normalized interaction frequency is represented as a heatmap for Hi-C data, the scale of which is shown in the upper-right corner and as a bar plot for NG-Capture C data, the scale of which is [0–70] as indicated. The yellow triangle indicates the viewpoint (TGFB2 TSS) where the NG-Capture C probes were designed. The peaks indicate regions of interaction with the TGFB2 promoter (PIRs). The positions of the PIR centers relative to the TGFB2 TSS are indicated in kb. Note that the signal was strongly trimmed at the level of the viewpoint for clearer visualization of the PIRs. The genes transcribed on the forward strand are shown in black, whereas those transcribed on the reverse strand are indicated in red. The black arrows in the Hi-C data indicate the interactions identified in HMECs that correspond to the TGFB2 PIRs identified in MDA-MB-321 cells. B Molecular characterization of the TGFB2 PIRs. NG Capture-C data obtained in the presence (siCTL condition; purple) or the absence of Fra-1 (siFra-1 condition; green) were aligned with H3K4me3-, H3K4me1-, H3K27ac-, H3K36me3, Pol II-, CTCF-, p300/CBP- and Fra-1 ChIP-seq data as well as with ATAC-seq data. The TGFB2 PIRs are indicated by vertical grey bars, as well as by blue boxes at the bottom of the figure. Normalized read counts are indicated between brackets. All other indications are as in (A). NG Capture-C data were obtained in 3 independent experiments using MDA-MB-231 cells transfected with either siCTL or siFra-1 for 72 h. The 3 NG Capture-C experiments using siCTL, on the one hand, and the 3 NG Capture-C experiments using siFra-1, on the other hand, were merged, as they gave highly similar results (average Pearson correlation coefficient of 0.96)