Fig. 5: Uncovering hb transcription kinetics through time-resolved single-molecule mRNA statistics. | Nature Communications

Fig. 5: Uncovering hb transcription kinetics through time-resolved single-molecule mRNA statistics.

From: Deep learning-based high-resolution time inference for deciphering dynamic gene regulation from fixed embryos

Fig. 5

a Schematic of the theoretical pipeline for deciphering unsteady-state transcription kinetics. Time inference for multiple smFISH-labeled fixed embryos enables reconstructing the evolution of single-cell mRNA signals (left), which were fitted to a time-dependent two-state transcription model (right). The mRNA signal at a time point is influenced by kinetic parameters within a preceding time window. b Histograms of nascent hb mRNAs at individual anterior gene loci (0.25–0.35 EL) over time in nc13. Data from n = 63 WT embryos were binned along the time axis (bin size: 0.5 min, step size: 0.5 min). All histograms were simultaneously fitted to the time-dependent two-state transcription model. c Percentage of activatable gene loci as a function of time during nc11–13. Data from various AP positions (0.2–0.4 EL) were averaged and fitted with a trapezoidal curve. The rising, plateau, falling, and silent phases of the trapezoidal curve for nc12 are highlighted in different colors. d Comparison of each trapezoidal phase across nc11–13. e Spatiotemporal profile of gene activation rate across nc11–13, for the AP position range of 0.05–0.55 EL. f Promoter activation rate and nuclear Bcd concentration at three distinct AP positions as functions of time in nc13. Dashed lines mark the period during which the Bcd concentration reaches its maximum, while the promoter activation rate continues to rise. Horizontal square bracket marks the period for subsequent steady-state analysis. g Schematic of cooperative Bcd binding-induced gene activation. h Steady-state promoter activation rate at different AP positions (0.20–0.55 EL) during 4.4–6.3 min in nc13 was plotted against nuclear Bcd concentration and fitted to a Hill function. i Unsteady-state promoter activation rate within the marked time period in (f) (2.8–4.2 min, 0.45 EL) was plotted against time and fitted to an exponential function. Source data are provided as a Source Data file.

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