Spotted-glass microarrays and Serial Analysis of Gene Expression (SAGE) have been combined successfully to identify downstream targets of FIGLA. Taking advantage of Figla null mice and the NIA 22K microarray that contains elements enriched for expression in oocyte and early development, ovarian gene expression was profiled at four embryonic time points from E12.5 to newborn. However, microarrays are limited by the elements spotted on glass during their fabrication. Therefore, to broaden the search for potential direct or indirect downstream gene targets, SAGE libraries were constructed from poly(A)+ RNA isolated from newborn normal and Figla null ovaries. A 10 base tag immediately adjacent to the 3 prime most Sau3A1 restriction enzyme cleavage site was used to identify both up-regulated and down-regulated transcripts. The further characterization of the genes that are differentially regulated by FIGLA should prove useful in defining developmental pathways that affect the postnatal female germ cell. These targets represent not only genes that affect folliculogenesis and fertilization, but also maternal effect genes required for successful completion of early mouse development.[unreadable] [unreadable] In an alternative approach to identify additional downstream targets of FIGLA, two-dimensional gel electrophoresis was used to compare the protein expression profiles of newborn ovaries isolated from normal and Figla null mice. Differentially expressed proteins were identified by microscale mass spectrometry and differences were confirmed at a transcriptional level by quantitative RT-PCR. Unexpectedly, twenty testis-specific proteins were over-expressed in Figla null newborn ovaries suggesting that FIGLA is not only an activator of oocyte-specific genes, but also a repressor of testis-specific genes, during female gonadogenesis. To further investigate this hypothesis, transgenic mouse lines ectopically expressing FIGLA in male germ cells were established. Although fertile, transgenic male mice expressing FIGLA had decreased fecundity and as mice aged, vacuoles were sporadically observed within seminiferous tubules consistent with patches of germ cell apoptosis. Collectively, these data indicate that FIGLA plays a critical role as the transcriptional activating of oocyte-specific and repressor of testis-specific genes necessary for successful development of the female gonad.