Genome‐wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling

FoxO transcription factors, inhibited by insulin/insulin‐like growth factor signalling (IIS), are crucial players in numerous organismal processes including lifespan. Using genomic tools, we uncover over 700 direct dFOXO targets in adult female Drosophila . dFOXO is directly required for transcription of several IIS components and interacting pathways, such as TOR , in the wild‐type fly. The genomic locations occupied by dFOXO in adults are different from those observed in larvae or cultured cells. These locations remain unchanged upon activation by stresses or reduced IIS, but the binding is increased and additional targets activated upon genetic reduction in IIS. We identify the part of the IIS transcriptional response directly controlled by dFOXO and the indirect effects and show that parts of the transcriptional response to IIS reduction do not require dfoxo . Promoter analyses revealed GATA and other forkhead factors as candidate mediators of the indirect and dfoxo ‐independent effects. We demonstrate genome‐wide evolutionary conservation of dFOXO targets between the fly and the worm Caenorhabditis elegans , enriched for a second tier of regulators including the dHR96 / daf‐12 nuclear hormone receptor. Synopsis Forkhead Box‐O (FoxO) transcription factors are crucial players in numerous cellular and organismal processes including metabolism, stress protection, cellular differentiation, cell‐cycle arrest, apoptosis and lifespan. FoxOs are regulated by a number of signalling pathways, including negative regulation by insulin/insulin‐like growth factor signalling (IIS) (Partridge and Bruning, 2008 ; Salih and Brunet, 2008 ). The fruit fly Drosophila melanogaster has a single FoxO orthologue—dFOXO. dFOXO is capable of extending fly lifespan, as well as being required for lifespan extension in response to downregulation of IIS (Giannakou et al , 2004 ; Hwangbo et al , 2004 ; Slack et al , 2011 ). To further our understanding of dFOXO biology, we uncover over 700 direct dFOXO targets in the adult female fly, both in the wild‐type fly and in a mutant with reduced IIS activity. dFOXO is directly required for transcription of several components of IIS and interacting pathways, such as the gene encoding the target of rapamycin (TOR) kinase, in the wild‐type fly. Indeed, the removal of dFOXO results in reduced signal through these pathways. The genomic locations occupied by dFOXO in adults are different from those observed by others in larvae or cultured cells (P