Fig. 1
Promoter-proximal paused Pol II is established at DV-regulated genes prior to ZGA but is released into elongation in a tissue-specific manner. a Schematic of embryonic DV patterning. From an initially transcriptionally inert naïve embryo (nuclear cycle (nc) 7–9, 60–80 min (min) after egg laying (AEL)), a dorsoventral (DV) nuclear gradient of the maternally supplied transcription factor Dorsal (Dl) (nc 10–13, 1.5–2.5 hours (h) AEL) specifies cell fates at zygotic genome activation (ZGA) (nc 14, 2.5–3.5 h AEL). Distinct transcriptional programs initiated by the absence of Dl dorsally, moderate nuclear Dl laterally, and high nuclear Dl ventrally lead to cell specification into dorsal ectoderm, neuroectoderm, and mesoderm, respectively. Disrupted Dl gradient formation in Toll signaling mutants produces embryos composed entirely of presumptive dorsal ectoderm (gd7), neuroectoderm (Tollrm9/rm10), and mesoderm (Toll10B). b Images of whole-mount in situ hybridization in wild-type and Toll mutant embryos (2–4 h AEL) with probes hybridized to mRNAs of representative DV-regulated genes (dpp, ind, and twi). c Schematic of the experimental design to study spatio-temporal transcriptional dynamics during DV patterning. PRO-seq was performed on naïve wild-type embryos (nc 7–9, 60–80 min AEL) and Toll mutant embryos at ZGA (nc 14, 2.5–3 h AEL) and after gastrulation (> nc 14, 4.5–5 h AEL). d Genome browser shots of stranded PRO-seq signal (RPKM ×103) at dpp, ind, and twi. Promoters are shaded gray. e Pausing index (PI) of DV and non-DV-regulated genes from qPRO-seq in wild-type naïve (1 h) embryos and f PRO-seq in Toll mutants. g PI of DV-regulated genes partitioned by the tissue of expression from PRO-seq in Toll mutants. h Metagene plots of Toll mutant PRO-seq signal at DV-regulated genes. Significant differences in the PI between DV and non-DV genes are from the Wilcoxon rank-sum and signed-rank tests and indicated by asterisks, * = P < 0.05, ** = P < 0.01, *** = P < 0.001