The H3K9 methyltransferase SETDB1 maintains female identity in Drosophila germ cells by repressing expression of key spermatogenesis genes

The preservation of germ cell sexual identity is essential for gametogenesis. Here we show that H3K9me3-mediated gene silencing is integral to female fate maintenance in Drosophila germ cells. Germ cell-specific loss of the H3K9me3 pathway members, the trimethyltransferase SETDB1, its binding partner WDE, and the H3K9 binding protein HP1a, cause the inappropriate expression of testis genes. SETDB1 is required for H3K9me3 accumulation on a select subset of the silenced testis genes. Interestingly, these SETDB1-dependent H3K9me3 domains are highly localized and do not spread into neighboring loci. Regional deposition is especially striking at the phf7 locus, a key regulator of male germ cell sexual fate. phf7 is primarily regulated by alternative promoter usage and transcription start site (TSS) selection. We find H3K9me3 accumulation is restricted to the silenced testis-specific TSS region in ovaries. Furthermore, its recruitment to phf7 and repression of the testis-specific transcript is dependent on the female sex determination gene Sxl. These findings demonstrate that female identity is secured by a pathway in which Sxl is the upstream female-specific regulator, SETDB1 is the required chromatin writer and phf7 is one of the critical SETDB1 target genes. This function of SETDB1 is unrelated to its canonical role in piRNA biogenesis and silencing of transposable elements. Collectively our findings support a novel model in which female fate is preserved by deposition of H3K9me3 repressive marks on key spermatogenesis genes and suggest that this strategy for securing cell fate may be widespread.