In recent years, the contribution of gut to health and disease, as well as the mechanisms important for gut homeostasis, like the maintenance of intestinal stem cells, have just began to be unraveled. Due to its general importance, studies addressing intestinal organization and physiology and, more generally, the question of how this organ functions as a whole, will become one of the most promising areas of research. In all animals, the mature gut is characterized by a succession of distinct compartments, which all fulfil important physiological function. However, how gut compartmentalization and the specialization of the different regions are controlled is largely unsolved in both Drosophila and mammals. The host lab has recently defined different sub-domains of the adult Drosophila midgut using both morphological and genetic criteria. This proposal aims to further unravel gene regulatory networks that control formation and function of each compartment, using a combination of state-of-the-art genetic, genomic, molecular and computational approaches. First, cis-regulatory elements (CREs) specific for different gut compartments will be systematically identified using ChIP-seq; second, key transcription factors interacting with compartment-specific CREs will be elucidated by yeast one-hybrid screens; third, the function of key transcriptional regulators in gut formation and maintenance, in particular the HOX transcription factors, will be studied using molecular, biochemical and genetic tools; and finally, I will apply computational tools to globally predict compartment-specific CREs based on the co-occupancy of key transcription factors identified above. This study will significantly advance our understanding of the mechanisms underlying the gut function, and will also have a major impact on understanding regulatory programs crucial for proper gut function in mammals.