Lissencephaly-1 gene is known to play many roles during drosophila development, it regulates cyst division, oocyte nucleus migration and control germ stem cell self-renewal hence oocyte formation. In this study we investigated the differential expression of UAS lis-1 RNAi gene construct under the effect of five GAL4 drivers (Nos GAL4, Nub GAL4, Eve 3+7 GAL4, Kni GAL4, Ftz GAL4)on cuticle development. Results showed that Nos and Nub GAL4/UAS lis-1 RNAi have strong effect on abdominal segment development. Meanwhile, Eve 3+7, Kni and Ftz GAL4/UAS lis-1 RNAi showed moderate effect. Proteomic studies (protein- protein interaction) using bicoid (bcd) and even–skipped antibody were used for determining the effect of Nos GAL4/UAS lis-1 RNAi on the expression of maternal and zygotic genes during developmental process. Results showed that Nos GAL4/UAS lis-1 RNAi gene affected slightly on the distribution of the bicoid protein. On the other hand using even-skipped antibody showed alteration in the head length and stripe pattern comparing with control. The overall data showed that UAS lis-1 RNAi gene play an essential role in drosophila axis formation and can be considered as a zygotic effect.