Fig. 3: 4C-seq in SHFM3 patient fibroblasts reveals ectopic interactions involving LBX1 and BTRC, further supported by virtual 4C in mouse. | Nature Communications

Fig. 3: 4C-seq in SHFM3 patient fibroblasts reveals ectopic interactions involving LBX1 and BTRC, further supported by virtual 4C in mouse.

From: Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve split-hand/foot malformation type 3

Fig. 3

a Hi-C at the LBX1/FGF8 locus (hg19; chr10:102,668,128-103,840,922) derived from GM12878 cell50. TADs structures are similar between human and mouse. CTCF ChIP-seq from GM12878 cells62,63, orientation of CTCF binding sites and schematic of the human LBX1/FGF8 locus are shown below. Red arrow indicates a CTCF binding site in antisense orientation at the LBX1 centromeric TAD boundary present in mouse but not in human. Below is the normalized 4C-seq of human fibroblasts healthy control (grey) versus a SHFM3 patient carrying the duplication (green line) with viewpoints (VP) on FGF8, LBX1 and BTRC promoters. Data are shown as merged signal of n = 2 replicates. b (Left panel) 4C-seq integrated signal over a 125 kb region comprising the FGF8 regulatory elements that are duplicated. (Right panel) A zoom-in view from the 4C-seq showing the region used for the integrated signal (blue rectangle). We observed an increase of contacts between both LBX1 and BTRC promoters and the FGF8 regulatory elements which is not present in control regions (Supplementary Fig. 4). c Similar representation as in (a) showing the mouse CTCF and virtual 4C (generated from E11.5 limbs cHi-C maps from Fig. 2) tracks. Wild-type (WT) signal is shown in grey and Dup and Inv1 with a green and orange line, respectively. Data are shown as merged signal of n = 3 replicates. d (Left panel) Virtual-4C integrated signal over the 125 kb region comprising Fgf8 regulatory elements that are affected by the duplication and the inversion. (Right panel) A zoom-in view from the virtual-4C showing the 125 kb used for the integrated signal (blue rectangles). Black arrow highlights a gain of contact observed only for Lbx1 view point with the Fgf8 gene, outside of the region of interest. Gain of interactions is observed between both Lbx1 and Btrc promoters and the Fgf8 regulatory elements which is not present in control regions (Supplementary Fig. 4).

Back to article page