Incomplete sister chromatid separation is the mechanism of programmed chromosome elimination during early Sciara coprophila embryogenesis.

Sex in Sciara coprophila is determined by maternally supplied factors that control the number of paternal X chromosomes eliminated during the syncytial embryonic divisions. Confocal microscopy and FISH demonstrate that the centromeres of the X chromosomes separate at anaphase and remain functional during the cycle in which the X chromosomes are eliminated. However, a region of the sister chromatids fails to separate and the X chromosomes remain at the metaphase plate. This indicates that failure of sister chromatid separation is the mechanism of chromosome elimination. Elimination of the X chromosomes requires the presence of a previously discovered Controlling Element that acts in cis during male meiosis. Using an X-autosome translocation, we demonstrate that the Controlling Element acts at-a-distance to prevent sister chromatid separation in the arm of an autosome. This indicates that the region in which sister chromatid separation fails is chromosome-independent. Although chromosome elimination occurs in all somatic nuclei and is independent of location of the nuclei within the embryo, the decision to eliminate is made at the level of the individual nucleus. Programmed X chromosome elimination occurs at different cycles in male and female embryos. These observations support a model in which elements on the X chromosome are titrating maternally supplied factors controlling the separation of sister X chromatids.