Appendix 1—figure 3. Expression of runt at phase 2 versus phase 3.

Relative expression of runt and other pair-rule genes (A, B – hairy; C, D – odd; E, F – eve; G, H - ftz) is shown in late phase 2 embryos (A, C, E, G) and in early phase 3 embryos (B, D, F, H). Individual channels are shown to the right of each whole embryo double channel image (runt bottom, other gene top). Other panels show blow-ups of expression in stripes 2–6 (individual channels, double channel image, and thresholded double channel image). runt expression is always shown in green. runt primary stripes are out of phase with hairy (A) but runt secondary stripes (asterisks in B) emerge within domains of hairy expression. runt expression overlaps with odd and eve at phase 2 (C, E) but not phase 3 (D, F). runt expression overlaps with ftz at both phase 2 and phase 3 (G, H). Arrowheads in (A) point to clear gaps between the posterior boundaries of the runt stripes and the anterior boundaries of the hairy stripes. Scale bars = 50 μm. See text for details.

DOI: http://dx.doi.org/10.7554/eLife.18215.028

Appendix 1—figure 3—figure supplement 1. Model for the regulation of runt transcription at phase 2 versus phase 3.

Model for the differential regulation of runt expression by pair-rule proteins at late phase 2 (A, B) versus early phase 3 (C, D). (A, C) Schematic diagrams showing the expression of runt relative to potential regulators. The horizontal axis represents an idealised portion of the AP axis (~12 nuclei across). The grey vertical lines demarcate a double parasegment repeat (~8 nuclei across). Lighter red and green sections in (C) represent fading Eve and Runt protein. (B, D) Inferred regulatory interactions. Separate regulatory logic is shown for the expression of the primary (1ary) stripes and the secondary (2ary) stripes, because they are driven by separate enhancers (see text for details). Hammerhead arrows represent repressive interactions. Solid black arrows represent interactions that are currently in operation; dashed grey arrows represent those that are not. At each stage, runt is expressed only where its current repressors are absent. See Appendix 1—figure 3 for staged relative expression data. Note that the expression patterns of potential regulators diagrammed in this figure represent protein distributions, which often differ slightly from transcript distributions due to time delays inherent in protein synthesis and decay (see Figure 6).

DOI: http://dx.doi.org/10.7554/eLife.18215.029