Depression is a complex, heterogeneous disorder and a leading contributor to the global burden of disease. Most previous research has focused on individual brain regions and genes contributing to depression. However, emerging evidence in humans and animal models suggests that dysregulated circuit function and gene expression across multiple brain regions drive depressive phenotypes. Here, we performed RNA sequencing on four brain regions from control animals and those susceptible or resilient to chronic social defeat stress at multiple time points. We employed an integrative network biology approach to identify transcriptional networks and key driver genes that regulate susceptibility to depressive-like symptoms. Further, we validated in vivo several key drivers and their associated transcriptional networks that regulate depression susceptibility and confirmed their functional significance at the levels of gene transcription, synaptic regulation, and behavior. Our study reveals novel transcriptional networks that control stress susceptibility and offers fundamentally new leads for antidepressant drug discovery. •A large-scale multi-brain region transcriptomic cohort to probe stress susceptibility•Reveals susceptible and resilient transcriptional networks across brain regions•Identifies many novel hub genes that emerge in susceptible mice•In vivo validation of key regulators at molecular, synaptic, and behavioral levels Molecular mechanisms of dysregulated circuit function in depression are poorly understood. Employing integrative network analysis of large-scale RNA sequencing data, Bagot et al. identify distinct inter-regional transcriptional networks regulating depression susceptibility versus resilience. In vivo validation of networks suggests novel antidepressant targets.