Fig. 5: ecDNA context is critical for EIE 14 enhancer activity.
From: Enhancer activation from transposable elements in extrachromosomal DNA
a, Schematic outlining the COLO320DM cell line as having high copy number and high ecDNA levels, versus the HSR cell line, which has high copy number but low ecDNA. b, RNA-FISH labelling for EIE 14 and MYC exon 2 transcription in COLO320 DM and HSR. Median transcripts for EIE 14 are 4 and 0 for the DM and HSR cells (two-tailed Wilcoxon ranksum P = 8.22 × 10−94), respectively. DM cells have a median of 14 MYC transcripts, and HSR cells have a median of 8 transcripts per cell (two-tailed Wilcoxon ranksum P = 2.18 × 10−66). n = 712 cells (DM) n = 681 (HSR) across two biological replicates. Scale bars, 8 μm. c, Luciferase enhancer assay schematics and fold change in luciferase signal driven by either MYC or TK promoter normalized to promoter-only construct. n = 4 biological replicates. EIE 14 compared with positive control (PVT1 positive control from ref. 20). P values obtained from two-tailed unpaired t-test. Error bars are standard deviations from the mean. d, Schematic outlining EIE 14 as a translocation event in healthy patients where EIE 14 is normally inactive across annotated cell lines (see a). EIE 14 gains regulatory potential when it is amplified within ecDNA as a consequence of translocation near MYC. EIE 14 can then act as a regulator of MYC in both cis and trans contacts within and between ecDNAs.
