A gene toolbox for monitoring autophagy transcription

Autophagy is a highly dynamic and multi-step process, regulated by many\r\nfunctional protein units. Here, we have built up a comprehensive and\r\nup-to-date annotated gene list for the autophagy pathway, by combining\r\npreviously published gene lists and the most recent publications in the\r\nfield. We identified 604 genes and created main categories: MTOR and\r\nupstream pathways, autophagy core, autophagy transcription factors,\r\nmitophagy, docking and fusion, lysosome and lysosome-related genes. We\r\nthen classified such genes in sub-groups, based on their functions or on\r\ntheir sub-cellular localization. Moreover, we have curated two shorter\r\nsub-lists to predict the extent of autophagy activation and/or lysosomal\r\nbiogenesis; we next validated the ``induction list{''} by Real-time PCR\r\nin cell lines during fasting or MTOR inhibition, identifying ATG14,\r\nATG7, NBR1, ULK1, ULK2, and WDR45, as minimal transcriptional targets.\r\nWe also demonstrated that our list of autophagy genes can be\r\nparticularly useful during an effective RNA-sequencing analysis. Thus,\r\nwe propose our lists as a useful toolbox for performing an informative\r\nand functionally-prognostic gene scan of autophagy steps.