Fig. 4: Differential RNA dynamics by gene function and posttranscriptional characteristics.

a, UMAP representation (left) and heatmap (right) showing the gene clustering using all 12 estimated parameters across cell cycle. Color in the heatmap represents the parameter-wise z-score normalized value. b, Pathway enrichment analysis of genes in each cluster in a using DAVID. c, Left, visualization of cytoplasmic RNAs of Clusters 2 and 4 in representative cells across pulse-chase timepoints. Scale bar, 10 µm. Right, density plot showing the distributions of γ values of genes in clusters 2 and 4. d, Diagram illustrating two possible mechanisms of reverse mRNA translocation (γ) at the G1 phase of cluster 4 genes: directed RNA transport and localized RNA degradation. e, Boxplots comparing the four parameters estimated for m⁶A and non-m⁶A genes. Units of α is RNA concentration per hour, where RNA concentration is defined by copies per voxel (voxel = 200 nm × 200 nm × 350 nm). Units of β, λ and γ are per hour. n = 476 genes for m⁶A-modified and 89 genes for non-m⁶A-modified. Data shown as means (notches), 25–75% quartiles (boxes) and ranges (vertical lines). **P < 0.01, two-sided Wilcoxon test in c and e.