Fig. 5: Three-state promoter kinetics reveal a unified scheme of P1 and P2 regulation.

a Histograms of nascent P1–5′UTR (upper) and P2–3′UTR (lower) signals at individual hb gene loci in different position ranges (single embryo, the center of each position range is indicated above the histogram). Each histogram was fitted to a three-state transcription model (right). b Histograms of nascent P1–5′UTR (upper) and P2–3′UTR (lower) signals at active sister loci in the position range of 0.2–0.4 EL. Each histogram was fitted to two Poisson distributions. Data pooled from seven embryos at nc13. Insets, images of a single anterior nucleus with active sister loci pairs. c Promoter activation rates for P1 and P2 estimated from five embryos at nc12 (binned along the AP axis, bin size: 0.1 EL, step size: 0.01 EL) were plotted against nuclear Bcd concentration and fitted to Hill functions. d, e The Hill coefficients (d) and concentration thresholds (e) of promoter activation rates for P1 and P2 during nc11–13. f The transcription initiation rates of the two active states for P1 and P2 during nc11–13. g The contributions of states 1 and 2 to P1 and P2 transcription in the position range of 0.2–0.4 EL during nc11–13. h P1 activation rates as functions of the AP position for different constructs at nc12 (data from 4 embryos for each reporter construct, bin size: 0.1 EL, step size: 0.02 EL). Data were normalized and compared between the distal- or proximal-enhancer-removed constructs and the control. i Schematic of P1 and P2 regulation by cooperative Bcd binding at the proximal and distal enhancers. j The joint distribution of nascent P1–5′UTR and P2–3′UTR signals at individual hb gene loci in the position range of 0.2–0.4 EL compared with model prediction. Data pooled from 17 embryos during nc11–13. White circles, individual loci. Color code, probability estimated from a unified model of P1 and P2 transcription. d–g Data are presented as mean ± s.e.m. n = 5, 5, and 7 biologically independent embryos at nc11–13, respectively. Source data are provided as a Source Data file.