Extended Data Fig. 3: Gene length effect on burst size and frequency and the effect of core promoter elements on mean expression and burst frequency. | Nature

Extended Data Fig. 3: Gene length effect on burst size and frequency and the effect of core promoter elements on mean expression and burst frequency.

From: Genomic encoding of transcriptional burst kinetics

Extended Data Fig. 3

a, b, Scatter plots of median burst size (a) and frequency (b) compared to median gene length. Genes were binned (50 genes per group). c, Box plot of genes binned according to gene loci length (20 genes per group). For each bin, we ranked genes according to their transcript lengths and calculated the gene-level difference to the median burst size of that bin. We see no effect from differing transcript lengths in estimated burst size. Box plots are as in Extended Data Fig. 2. d, e, Mean expression (d) and burst frequency (e), ordered and coloured for genes based on their core promoter elements. (Complementing the analysis presented in Fig. 2b, but with mean expression and burst frequency as dependent variables.) The results of the linear regressions are shown in Supplementary Table 1 (n = 7,186 genes). f, Scatter plot of burst frequency and size of genes with each dot colour by their mean expression level. g, Box plots showing the inferred burst size for genes separated according to the presence of core promoter elements, and further grouped into five equally sized bins (quintiles, QU1–QU5) according to gene loci lengths. No TATA or initiator: n = 4,397 genes (2,585, 1,124, 635, 36 and 17 in each quintile, respectively), Only initiator: n = 2,035 genes (942, 531, 442, 74 and 46 in each quintile, respectively), Only TATA: n = 359 genes (129, 126, 58, 31 and 15 in each quintile, respectively), TATA and initiator: n = 144 genes (53, 45, 24, 19 and 3 in each quintile, respectively).

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