Fig. 2
From: Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data
a Illustration of dynamic equilibrium between production and decay of RNA. PRO-seq (Pi) can be used to measure production and RNA-seq (Ri) to measure the resulting equilibrium RNA concentration. At steady state, the production and decay rates must be equal, allowing for estimation of a quantity proportional to RNA half-life (T1/2PR) by the ratio Ri/Pi (see the “Methods” section). Illustration adapted from [33]. b Scatter plot with density contours for (log2) half-lives estimated by the PRO-seq/RNA-seq method (T1/2PR, x-axis) vs. those estimated by TimeLapse-seq (Schofield et al. [20]) (T1/2TLS, y-axis) for 4351 TUs assayed by both methods in K562 cells. The T1/2PR values are unit-less, whereas the T1/2TLS values are expressed in hours. ρ = Spearman’s rank correlation coefficient. c Empirical cumulative distribution functions (eCDFs) for (log2) estimated RNA half-lives, T1/2PR, for ribosomal proteins (n = 119), zinc-finger proteins (n = 827), and other genes (n = 7216; p < 3.99e−15, Kolmogorov–Smirnov [K-S] test). d Similar eCDFs for mRNAs predicted to be targets (n = 668) of miR-182-5p vs. non-targets (n = 7494, p = 4.75e−8, K-S test). In c and d, shading indicates 95% confidential intervals as estimated from 1000 bootstrap replicates