Autophagy is a fundamental catabolic process that plays a central role in health and disease. An efficient autophagic process relies on the cooperation of two distinct types of organelles: the autophagosome and the lysosome. We have identified a gene network that regulates the biogenesis and function of both organelles. Our findings reveal an important role of transcription in the regulation of starvation-induced autophagy, and link lysosomal biogenesis to autophagy.