Macroautophagy is an evolutionarily conserved cellular process involved in the clearance of proteins and organelles. Although the cytoplasmic machinery that orchestrates autophagy induction during starvation, hypoxia, or receptor stimulation has been widely studied, the key epigenetic events that initiate and maintain the autophagy process remain unknown. Here we show that the methyltransferase G9a coordinates the transcriptional activation of key regulators of autophagosome formation by remodeling the chromatin landscape. Pharmacological inhibition or RNA interference (RNAi)-mediated suppression of G9a induces LC3B expression and lipidation that is dependent on RNA synthesis, protein translation, and the methyltransferase activity of G9a. Under normal conditions, G9a associates with the LC3B, WIPI1, and DOR gene promoters, epigenetically repressing them. However, G9a and G9a-repressive histone marks are removed during starvation and receptor-stimulated activation of naive T cells, two physiological inducers of macroautophagy. Moreover, we show that the c-Jun N-terminal kinase (JNK) pathway is involved in the regulation of autophagy gene expression during naive-T-cell activation. Together, these findings reveal that G9a directly represses genes known to participate in the autophagic process and that inhibition of G9a-mediated epigenetic repression represents an important regulatory mechanism during autophagy.A utophagy is an evolutionarily conserved catabolic process in eukaryotes that involves lysosomal degradation of cellular components, including long-lived proteins and organelles. There are four main forms of autophagy: macroautophagy (referred to here as autophagy), selective autophagy, microautophagy, and chaperone-mediated autophagy (1-4). Autophagy serves as an adaptive response to protect cells or organisms during periods of cellular stress, such as nutrient deprivation. In addition, autophagy can participate in several cellular and developmental processes, including homeostasis, clearance of intracellular pathogens, and immunity (1). Due to its fundamental importance for cellular survival, autophagy regulation has been implicated in several human diseases, such as cancer and neurodegenerative disorders (2, 5).Autophagy initiation involves the de novo synthesis of a double-membrane structure known as the phagophore, which ultimately elongates and closes to sequester cytoplasmic proteins and organelles, forming the autophagosome. The autophagosome subsequently undergoes a stepwise maturation process that culminates in its fusion with acidified endosomal/lysosomal vesicles, resulting in the degradation of its contents into useful biomolecules (2). A screen of yeast mutants unable to survive under nitrogen deprivation characterized a network of autophagy-related (ATG) genes (6). Mammalian homologues of these ATGs were later identified and shown to participate during distinct steps of autophagy. For example, microtubule-associated protein light chain 3 (LC3B) undergoes lipidation and is recruited to the pha...