Figure 3: CB-mediated inter-chromosomal interactions influence histone and U RNA gene expression.

(a) Representative 4C-seq contact profile of inter-chromosomal, CB-dependent interactions using a RNU1 bait sequence (chromosome 1) for HeLa WT (pink) and siTCAB1 (blue) treatments at the HIST1 locus on chromosome 6. A number of expressed histone genes are enriched within this region (dotted lines) which were determined to decrease following siTCAB1 and siUSPL1 (green) treatment and poorly expressed in primary cervical epithelial cells (purple) by small RNA-seq. y-axis displays the read counts/genome fragment. (b,c) 4C-seq contact profile for the SNORD3A (U3 snoRNA, b) and RNU2 (U2 snRNA, c) loci on chromosome 17 using a RNU1 bait in HeLa cells. Control (HeLa WT, pink) and siTCAB1 (blue) are shown, as well as small RNA-seq profile for SNORD3A in control, siTCAB1, siUSPL1 (USPL1kd, green) and primary cervical epithelial cells (purple). y-axis displays the read counts/genome fragment. Several genes of interest were also located in this region, denoted by arrows (orange=RNA-seq expression change following TCAB1 or USPL1kd, blue=splicing defect detected, grey=no change). (d) Validation of a selection of histone genes by qRT–PCR normalized to β-actin (yellow=primary D551 cells, red=HeLa siControl, blue=HeLa siTCAB1). n=2, *P<0.05, ^#P<0.01, ^§P<0.001 compared with HeLa siControl, significance was assessed by Student’s t-test. Error bars represent s.e.m.