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Fig. 7 | Genome Biology

Fig. 7

From: Regulatory landscape fusion in rhabdomyosarcoma through interactions between the PAX3 promoter and FOXO1 regulatory elements

Fig. 7

The PAX3 promoter interacts with FOXO1 sequences in a patient-derived ARMS cell line. 4C-seq profiles on (a) the PAX3 and (b) the PAX3-FOXO1 loci obtained using the PAX3 promoter as a viewpoint in the RMS cell line. The locations of the promoter and the translocation breakpoint in are indicated. In (b), the first row represents the derivative t(2:13) chromosome 4C-seq profile. Green and orange boxes indicate reads mapped to Chr2 or Chr13, respectively. The second row shows the location of the fusion PAX3:FOXO1 gene and other coding sequences. The third row indicates the locations of 4C-peaks defined using the Peak Calling algorithm; the downstream limit was taken as the TAD boundary defined in the previous experiment. The fourth and fifth rows show H3K4me1 and H3K27ac marks in different tissues, respectively. The sixth row is the transcription factor-ChIP track from UCSC. The seventh row indicates vertebrate conservation. c Sequence-paired 4C-seq tracks on the FOXO1/FoxO1 locus from mouse embryos (green) and the RMS cell line (red) showing the location of ECRs shared between human, mouse and opossum genomes as shown in Additional file 1: Figure S3. d Correlation between the 4C-seq signal in the FOXO1/FoxO1 loci from mouse embryos and RMS human cells. For each conserved element, the 4C-seq signal in human cells corresponding to this region is plotted against the 4C-seq signal from mouse embryos in the orthologous region. The red dashed line represents the linear regression line

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