Figure 1.
Transcript- and genomic level validation of the fusion genes.
A. Validation of the fusion genes from BT-474 and MCF-7 on the cDNA level by RT-PCR. B. Genomic DNA sequence at the fusion gene break point of THRA-AC090627.1 (top), TOB1-SYNRG (middle) and MED1-ACSF2 (bottom). Chromosomal positions of the fusion break points are indicated by black arrows. Gene and transcript structures as well as nucleotide sequences at the break points are drawn in blue for 5′ and in red for 3′ partner genes. Gene structures above and below chromosome coordinates imply forward and reverse strand, respectively. Transcript structures of gene fusions are indicated below the gene structures and connected with gray lines. Genomic DNA sequence at the break point (indicated by asterisk) is shown below the transcript structures. Black color indicates nucleotides that match to both (THRA-AC090627.1, MED1-ACSF2) or neither partner genes (TOB1-SYNRG).
Table 1.
Identified and validated fusion gene candidates.
Figure 2.
Genomic rearrangements underlying fusion gene formation.
Circos plots illustrating chromosomal translocations in BT-474 (upper) and MCF-7 (lower). Chromosomes are drawn into scale around the rim of the circle and data are plotted on these coordinates. Intrachromosomal (red) and interchromosomal (blue) fusions are indicated by arcs. Copy number profiles are plotted in the inner circle. Amplifications are shown in red and deletions in blue. N denotes the number of fusion genes per cell line.
Figure 3.
MED1 forms fusions with several partner genes.
Exonic expression of MED1 and its partner genes ACSF2, USP32 and STXBP4 is indicated by sequencing coverage (red). Copy number changes measured by aCGH (black lines) in reference to normal copy number (horizontal gray lines), and chromosomal positions (vertical red lines on chromosomes) are indicated. Transcript structures of wild type genes as well as gene fusions are indicated by red (MED1) and blue (ACSF2, USP32, STXBP4), and connected with lines of same color. Arrows show the 5′ 3′ direction of the genes.
Figure 4.
Exclusive expression of fusion partner genes.
Exonic expression of THRA in THRA-AC090627.1 (A) and MSI1 in GCN1L-MSI1 (B) is indicated by sequencing coverage (red). Copy number changes measured by aCGH (black lines) in reference to normal copy number (horizontal gray lines), chromosomal positions (vertical red lines on chromosomes) and fusion break points (vertical gray bars) are shown. Transcript structures are indicated below the aCGH profiles with the arrows pointing to the parts of the transcripts taking part in the fusions.
Figure 5.
Several fusion transcripts have multiple splice variants.
Five examples from BT-474 (A. THRA-AC090067.1, B. TOB1-SYNRG, C. TRPC4AP-MRPL45, D. MED1-STXBP4 and E. STX16-RAE1) are presented. Multiple splice variants are visible as RT-PCR bands, and schematically represented by the arrows to the left. Chromatograms show the actual cDNA sequence break points of the main predicted fusion isoforms, and are connected with lines to the corresponding RT-PCR bands. Gray arrows = coding sequence, white arrows = untranslated exon or 3′/5′ UTR, thin lines connecting exons = intronic regions. 5′ partner genes are represented by brown color, 3′ partner genes by green.