Fig. 2: A link between eccDNA formation and transcription. | Nature Communications

Fig. 2: A link between eccDNA formation and transcription.

From: EccDNA atlas in male mice reveals features protecting genes against transcription-induced eccDNA formation

Fig. 2

a Schematic overview of RNA samples sequenced in liver. PCA plot of RNA profiles between age groups, with the percentage of variance explained by PC1 and PC2 components shown in brackets. b Euclidean distance between all samples across 3 age groups (3-month: n = 6; 12-month: n = 5; 22-month: n = 6) in the PCA space, assessed using two-side t test. Significance (***) is shown if p < 0.001 (3-month vs. 12-month: p = 8.8e−05, 3-month vs. 22-month: p = 1.6e−06, 12-month vs. 22-month: p = 3.3e−05). The median is marked with a white line, with margins showing the interquartile range (IQR), whiskers extending up to 1.5 IQR, and outliers showing as individual data points. c Variance in the Sørensen-Dice Similarity Coefficient (SDC) assessing similarities between eccDNA profiles in each age group (see methods and Supplementary Fig. 5). Variance equality was tested using two-side F test. Significance (*) is shown if p < 0.05. d Schematic overview of RNA and eccDNA profiles showing variability increasingly different as liver aged. e Percentage of genes detected within eccDNA profiles and expressed in tissues and ages. Gray indicates genes detected in eccDNA profiles with no transcript detected. f–h Logarithmic eccDNA number per Mb for each gene as a function of normalized read counts per Mb of liver. LOESS regression fitted (colored line) with kernel 2-densities plotted. Residual Standard Error (RSE) is shown for each LOESS regression. i eccDNA level at the same gene expression level: (log2 (eccDNA count per Mb/normalized RNA count per Mb)) across age groups. The Kruskal–Wallis test was used to assess significant differences (3 vs. 12-month: p = 0.0061; 3 vs. 22-month: p = 1.4e−15, 12 vs. 22-month: p = 4.4e−10). The white bar represents median values (3-month = −7.99, 12-month = −7.79, 22-month = −7.24). j Heatmap shows the association of eccDNA with interested genomic features within 50 kb genome windows. eccDNA+: exits eccDNA in 50 kb windows. eccDNA−: does not exist.

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