Insulator BEAF32 regulates expression of tissue-specific genes and piRNA source loci in the Drosophila ovaries [ChIP-seq]
Background: 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. Drosophila insulator BEAF32 (Boundary Element-Associated Factor of 32 kD) is a component of chromatin complexes found in the open chromatin regions containing promoters of housekeeping genes. BEAF32 knockout impairs oogenesis and female fertility suggesting its specific functions during oogenesis Results: 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. Among upregulated genes there were not only BEAF32-associated genes suggesting direct and indirect mechanisms of BEAF32-mediated expression control. We discovered that BEAF32 occupied many ovary-specific gene promoters and acted as a positive regulator of the cell-cycle regulatory kinase Polo expression. To reveal the possible role of BEAF32 in the pathway mediated by Piwi-interacting RNAs (piRNAs) we performed an analysis of ovarian small RNAs in the BEAF32 null mutants and revealed a strong decrease in the production of piRNAs from the 3R subtelomeric region. Our data suggest that 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 upstream of flamenco, a largest piRNA source locus in the follicular cells, and is required for the cell-specific transcription of the flam locus. Conclusions: These findings suggest that BEAF32 represses the ectopic expression of developmental and tissue-specific genes in the ovaries. BEAF32 regulates polo kinase and other oogenesis-related genes. BEAF32 insulators have been revealed to play a specific ovarian role in the maintenance of piRNA-producing loci. Our results provide strong support for the importance of BEAF32 insulator protein in determining the proper landscape of tissue-specific gene expression and locus-specific function realization. Overall design: Deep-sequencing of chromatin immunoprecipitated genomic DNA on Drosophila melanogaster ovaries