CSN4^N mutant female germline stem cell (GSC) clones are lost from the niche much more quickly than wild type controls. No dramatic increase in apoptosis is seen in GSCs or cysts compared to controls but CSN4^N mutant GSCs produce fewer differentiated cysts than controls. Fewer CSN4^N mutant GSCs are undergoing mitosis (BrdU staining). The remaining CSN4^N mutant GSCs are able to differentiate correctly into germ cell cysts.

Females carrying CSN4^N germ-line clones generated using the produced by using the dominant-female-sterile - FLP/FRT technique, lay a few eggs during a short period of time starting some days after heat shock-induced recombination. Oogenesis in these germ-line clones is progressively disrupted at earlier and earlier stages following heat shock, until it is arrested at the first mitotic division. The resulting undifferentiated cysts have germ-cells with enlarged nuclei and defective fusome development. These polyploid, nondividing germ cells may be the germline stem cells: there are never more than three in a germarium, and they retain contact with somatic cells that probably correspond to the basal and terminal filament cells of normal germaria.

When homozygous somatic clones are made in the larval developing eye, eye cells are seen with markedly abnormal cellular morphologies.