Fig. 1

Identification of functional enhancer elements downstream of the inversion breakpoint. a The genomic location of the inversion breakpoint on chromosome 7q31 with the boundaries of the topological domain shown by green boxes [18]. Genes are depicted in blue. b Detailed view of the breakpoint with functional annotations from the ENCODE project [12] and UCSC genome browser [20]. The inversion breakpoint was mapped to position 114539340 of chromosome 7 in human genome build hg19 [11] (indicated by arrows). DNase hypersensitivity sites (DNase H) indicates regions of open chromatin. The darkness of the grey boxes is proportional to maximum signal strength of the DNase hypersensitivity in any investigated cell line. TF ChIP indicates sites that were occupied by TFs and the colour intensity is proportional to the amount of different TFs found at one site. The H3K4Me1 track indicates the presence of histone-3 lysine-4 mono-methylation in human cell lines. Pink peaks correspond to those found in NHEK cells (colorectal carcinoma) and orange peaks to those found in GM12878 (EBV transformed lymphoblast) cells. The investigated genomic elements are represented as black bars. Element 1 overlaps a DNase H site detected in 48 cell lines and 4 TFs. Element 2 overlaps a DNase H site detected in 17 cell lines and 1 TF. c-d Reporter constructs containing no enhancer (no element control), Element 1 (chr7: 114541370 – 114542201, hg19) and Element 2 (chr 7: 114550520 – 114551429, hg19) were transfected into HEK293 and SK-N-MC cells. After 2 days the luciferase activity was determined as described before [21]. The firefly luciferase activity was normalized to the activity of a co-transfected renilla luciferase control to determine the relative luciferase activity. The luciferase activity driven by the genomic elements was compared to that obtained from the control luciferase plasmid (minP). Element 1, but not Element 2 was able to enhance the activity and therefore the expression of the reporter gene. We performed two independent experiments of each three biological replicates. Significance was determined by an ANOVA followed by post-hoc Tukey test.*p < 0.05, ***p < 0.001. N.S.: not significant