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The twelve zinc finger Suppressor of Hairy-wing [Su(Hw)] protein binds thousands of sites in Drosophila genome and is essential for the function of the gypsy insulator. Loss of the globally expressed Su(Hw) protein causes female sterility due to tissue-specific defect limited to female germline. Using chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq), we determine the extent of tissue-specific binding of Su(Hw) in Drosophila ovary. We demonstrate that Su(Hw) binding sites (SBSs) are largely constitutively occupied in the germline and soma. Our analyses indicate that SBSs fall into several non-uniform classes, as determined by the partner protein distribution and DNA sequence conservation. Further, we show that only a subset of SBSs is required for the female fertility. These sites are maintained in the su(Hw)f zinc finger 10 mutant background, which is fertile but does not support gypsy insulator function. Together, our data are consistent with the model where Su(Hw) serves multiple regulatory roles in the genome, and contribute to understanding of how loss of a single zinc finger affects chromosome localization of a DNA binding protein. Examination of Su(Hw) localization in the ovaries of less than 6 hour old wild type and su(Hw)f mutant Drosophila females

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