Maternal effect genes are transcribed, and their mRNA translocated into the egg, during oogenesis. Maternal effect genes acts before any zygotic genes, which are encoded by the embryonic genome itself. The maternal phenotype determines the zygotic phenotype. Thus, a MEG+/- female will have all normal children even if the child’s phenotype is MEG-/- (due to mating with a MEG+/- male or MEG-/-). However, a MEG-/- female will be unable to have normal children because embryonic development will be defective. There are forty maternal effect genes in Drosophila, including:
| Region | Description | Maternal Effect Genes |
| Acron | Part of the head. | torso |
|---|---|---|
| Anterior | Head and thorax. | bicoid (bcd) |
| Posterior | Abdomen | nanos |
| Telson | Tail region. | torso |
A spacially restricted ligand activates the Torso RTK, which then initiates a phosphorylation cascade — involving Ras, Raf-1, MAP kinase kinase (MAPKK, aka MEK) and then MAP kinase (MAPK) — that inactivates transcriptional repressors at the two poles of the embryo. This is critical for terminal formation. Where RTK is most activated, huckebein and tailless transcription is activated; extending to where activation is reduced, tailless transcription (encoding tailless) is still activated.

Sex-lethal is a sequence-specific RNA binding protein that recognizes a specific UGUUUUUUU element in its target RNAs. It has a Β1,2,3 & 4 domains as well as RNA recognition motifs RRM1 and RRM2. The presence or absence of Sxl in an early embryo will determine whether it develops as a male or a female.
| Early Female Embryo | Late Female Embryo | |
| There is transcription from the Sxl PE promoter. An mRNA is encoded starting at the E1 exon. A functional Sxl protein is expressed. | The PL promoter is activated. Its ORF is different than PE and L3 now has a premature stop codon. However, Sxlearly binds near L3 to block U2Af from binding the 3′ splice site. Thus L3 (and its stop codon) is skipped in females. Functional Sxl is expressed. | |
| Early Male Embryo | Late Male Embryo | |
| No transcription from PE. No Sxl expressed. | The PL promoter is activated. There is no Sxlearly, so the stop codon in L3 leads to expression of a truncated and inactive Sxl. | |

The female produced Sex-lethal protein also regulates splicing of Transformer (Tra), the next gene downstream in the Sexual Differentiation Pathway.
An exon in Tra pre-mRNA has two 3’ splice sites. U2AF has higher affinity for the primary upstream 3’ splice site, so splicing occurs there. However, this polypyrimidine tract also contains a high affinity Sxl binding element allowing Sxl to bind if it is present.
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