Degradation regulates mRNA dynamics and can be approximated using the time delay between peak pre-mRNA and mature mRNA expression.

(A) Clustering of pre-mRNA (Ai) and mature (Aii) mRNA time series. Plots show the mean expression value at each time point for all mRNAs in a cluster and the shaded area shows the standard deviation. The intronic cluster ID (Ai) or mean half-life (Aii) is shown in the top left and the number of transcripts in each cluster in the bottom right. (B) Heatmaps of pre-mRNA and mRNA expression at the gene-level for the subset of zygotic transcripts, ordered by the time point of maximum pre-mRNA expression. (C) Schematic illustrating the estimation of temporal delays between pre-mRNA and mature mRNA peak times (Δt, arrows) by fitting and sampling from a GP. (D) Correlation of the delay between the peak of pre-mRNA and mature mRNA against inferred half-life (Pearson’s r = 0.56, p = 6.5 × 10−14 for testing non-correlation). Points representing transcripts are coloured by time delay category. (E) Confusion matrix comparing mRNAs categorised into short, medium, and long delays and their respective half-life categories. Numbers in the boxes indicate the fraction of mRNAs with a given delay in the corresponding half-life category. Underlying data can be found in S1 Data and S4 Table. GP, Gaussian process.