Short and long-term regulation of autophagy

Abstract: Autophagy is a conserved catabolic pathway triggered by stress conditions in which portions of the cytoplasm, damage organelles, misfolded proteins and intracellular bacteria are delivered and degraded in the lysosome/vacuoles. Thus, an efficient induction and completion of the process is required to ensure a proper homeostasis of the cell. Autophagy has been considered a cytoplasmic event where the role of the nucleus on the regulation of this pathway was underestimated. However, recent findings elicited the role of histone modifying enzymes on the transcriptional regulation of autophagy-related (ATG) genes. In line with those results, we focused on the role of the two histone modifying enzymes regulating the histone 3 lysine 36 (H3K36) trimethylation, Rph1/KDM4A and Set2/SETD2, on the regulation of autophagy. In paper I, we investigated the function of the histone demethylase, Rph1/KDM4 as a negative regulator of autophagy, whereas in paper II we uncovered the role of the histone methyltransferase, Set2/SETD2, as a positive transcriptional regulator of ATG genes, as the impact on the differential expression of ATG14 splice isoforms that results on the inhibition of the autophagosome-lysosome fusion. Moreover, in paper III, we identify that SETD2 inactivating mutations on clear cell renal cell carcinomas (ccRCC) lead to an aberrant ATG12-containing complexes and accumulation of free ATG12, which is associated with a differential expression of ATG12 isoforms and reduced autophagic flux. Whereas the previous studies report the involvement of histone modifying enzymes and on the short-term regulation of autophagy, we also aimed to decipher the epigenetic mechanism responsible for the long-lasting effects of autophagy. In paper IV, we found that short autophagy stimulus is associated with an upregulation of de novo DNA methyltransferase 3A (DNMT3A) responsible of an increase of DNA methylation on selected ATG genes. Eventually, this epigenetic memory involves a persistent decrease of baseline autophagy. Moreover, in paper V, we uncovered the mechanism upstream on the regulation of DNMT3A expression by ULK3-mediated phosphorylation and activation of GLI1. Overall, these insights bring light on novel mechanisms and signaling pathways controlling short and long-term transcriptional regulation of autophagy by histone modifying enzymes, alternative splicing and DNA methylation.