Insulator BEAF32 regulates expression of tissue-specific genes and piRNA source loci in Drosophila ovaries

Insulators are the multifunctional DNA binding proteins that perform architectural functions and regulate gene transcription. Although insulators have a well-established role in genome organization, it is still unclear how insulator proteins affect the control of tissue-specific processes. The Drosophila insulator BEAF32 (Boundary Element-Associated Factor of 32 kD) is a component of chromatin complexes found in open chromatin regions containing promoters of housekeeping genes. BEAF32 knockout impairs oogenesis and female fertility suggesting its specific functions during oogenesis.

To get a better understanding of BEAF32 roles in oogenesis, we first examined its ovarian binding targets and discovered an enrichment of its localization sites in the promoters of both housekeeping and tissue-specific genes. Differential expression gene analysis revealed that BEAF32 knockout resulted in abnormal activation of non-ovarian tissue-specific genes in the ovaries, implying that BEAF32 regulates tissue-specific patterns of gene expression. We discovered that BEAF32 occupied many ovary-specific gene promoters and acted as a positive regulator of expression for the cell-cycle regulatory kinase, Polo. To investigate the possible role of BEAF32 in the Piwi-interacting RNAs (piRNAs) pathway we analyzed ovarian small RNAs in BEAF32 null mutants and found a strong decrease in the production of piRNAs from the 3R subtelomeric region. Our data suggest that the BEAF32-containing chromatin complex located upstream of the subtelomeric repeats preserves transcriptional and chromatin integrity of this domain in the germline. BEAF32 was also found to localize upstream of flamenco, a major piRNA source locus in follicular cells, and to be required for cell-specific transcription of the flamenco locus.

Our findings suggest that BEAF32 coordinates multiple transcriptional regulatory functions important for Drosophila oogenesis. BEAF32 represses the ectopic expression of developmental and tissue-specific genes in the ovaries. BEAF32 regulates polo kinase and other oogenesis-related genes. We demonstrate here that BEAF32 play a specific ovarian role in the maintenance of piRNA-producing loci. Our results support an important role for the BEAF32 insulator protein in determining the proper landscape of tissue-specific gene expression.