During the first three hours, the Drosophila embryo develops as a syncycium: it consists of a single cell, which performs nuclear divisions. Nuclei migrate to the surface, where they initiate transcription depending on the presence or absence of factors that spread through the embryo by diffusion. A striped pattern is established along the anterior-posterior axis of the embryo. Before the onset of gastrulation, membranes protrude between the nuclei, giving rise to about 6000 cells. Patterning processes from now on are dependent on interactions between these cells.

Segment polarity genes start to be expressed in 14 stripes at the onset of gastrulation. As the expression of gap genes and pair rule genes fade away during gastrulation, the segment polarity genes now take over to stabilize and refine the striped pattern.

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