Extended Data Fig. 4: Transcriptional burst kinetics of lncRNAs and divergent promoters.
From: Transcriptional kinetics and molecular functions of long noncoding RNAs
(A-C) Density plots for burst frequencies (A) burst sizes (B) and mean expression (for allele-distributed UMIs) (C) for mRNAs and lncRNAs (showing the CAST allele). Dashed lines represent the median burst frequencies, sizes and mean expression for mRNAs and lncRNAs. The relative fold changes are annotated in grey. P-values represent a two-sided Wilcoxon test. (D) Scatter plot comparing estimated RNA half-lives for mouse ES cells (y-axis) and mouse fibroblast cells (x-axis). R represents the Spearman correlation. (E) Violin plots for RNA half-lives (left) and RNA decay rates (right) for mouse fibroblasts. P-values represent a two-sided Wilcoxon test. (F) Histogram showing the duration between two bursts from the same allele (CAST), for mRNAs and lncRNAs. Dashed lines represent the median duration between two bursts for mRNAs and lncRNAs. Grey line represents a duration of 24 hours between two bursts. (G,H) Scatter plot of mean expression (for allele-distributed UMIs) against the CV2 for lncRNAs and mRNAs for the C57 (G) and CAST (H) genomes. The top 50 ranked lncRNAs are marked in light blue (see Methods). The red dotted line denotes the lower expression cutoff for lncRNAs to be included in the analysis. (I,J) Histograms showing the distribution of median burst frequencies (I) and burst sizes (J) for sampled expression-matched sets of mRNAs (for lncRNAs identified in (H)). The p-values represent the outcome of the permutation test (n = 10,000, see Methods), (K) Schematic representation of divergent and unidirectional transcribing promoters. (L) Violin plots for mean expression of mRNAs (allele-distributed UMIs) for divergent and unidirectional promoters for the C57 and CAST alleles. The p-values represent a two-sided Wilcoxon test. Fold-change in medians: C57coding-coding = 1.31; C57coding-lncRNA = 1.27; CASTcoding-coding = 1.27 and CASTcoding-lncRNA = 1.29. (M) Violin plots for unidirectional and divergent promoters representing burst frequencies and burst sizes, for the CAST allele. P-values represent a two-sided Wilcoxon test. L,M, The center lines represent the medians, the interquartile limits indicate the 25th and 75th percentiles and the whiskers denote the farthest points at a maximum of 1.5 times the IQR.
