New transcriptional roles for the classic Drosophila insulator protein Suppressor of Hairy-wing

The Drosophila Su(Hw) protein is a multi-zinc finger DNA binding factor required for the gypsy insulator function. At the gypsy element, Su(Hw) recruits partners Centrosomal Protein of 190 kD (CP190) and Modifier of mdg4 67.2 kD isoform (Mod67.2), which are required for the enhancer blocking and barrier functions of the insulator. Our genome-wide studies have identified thousands of endogenous non-gypsy Su(Hw) binding sites (SBSs) in the Drosophila genome, constitutively occupied throughout development. Yet, only a third of these SBSs are associated with CP190 and Mod67.2, suggesting that the endogenous function of Su(Hw) may not necessarily involve the formation of a gypsy-like chromatin insulator. To understand the function of endogenous SBSs, we investigated the requirement for Su(Hw) during female germline development. To this end, we performed genomewide transcriptional analyses in su(Hw) mutant ovaries coupled with the genome-wide definition of ovary SBSs. We identified 93 direct targets of Su(Hw) regulation in the ovary, with 68% of these genes showing increased RNA accumulation when Su(Hw) is lost. Derepressed Su(Hw) targets are normally highly expressed in central nervous system, suggesting that Su(Hw) has a critical role in silencing neural genes in the nonneural tissues. We find that a single upregulated target gene is largely responsible for the female sterility of su(Hw) mutants. This gene encodes an elav family factor RNA binding protein 9 (Rbp9), and Su(Hw)-mediated repression of Rbp9 is required at a specific stage of oogenesis. Decreasing the levels of Rbp9 restores female fertility of su(Hw) null mutants. Further, we demonstrate that Su(Hw) is required for transcriptional activation of