A gene toolbox for monitoring autophagy transcription

Abstract

Autophagy is a highly dynamic and multi-step process, regulated by many functional protein units. Here, we have built up a comprehensive and up-to-date annotated gene list for the autophagy pathway, by combining previously published gene lists and the most recent publications in the field. We identified 604 genes and created main categories: MTOR and upstream pathways, autophagy core, autophagy transcription factors, mitophagy, docking and fusion, lysosome and lysosome-related genes. We then classified such genes in sub-groups, based on their functions or on their sub-cellular localization. Moreover, we have curated two shorter sub-lists to predict the extent of autophagy activation and/or lysosomal biogenesis; we next validated the “induction list” by Real-time PCR in cell lines during fasting or MTOR inhibition, identifying ATG14, ATG7, NBR1, ULK1, ULK2, and WDR45, as minimal transcriptional targets. We also demonstrated that our list of autophagy genes can be particularly useful during an effective RNA-sequencing analysis. Thus, we propose our lists as a useful toolbox for performing an informative and functionally-prognostic gene scan of autophagy steps.

Single-Cell Transcriptome Analysis Reveals Embryonic Endothelial Heterogeneity at Spatiotemporal Level and Multifunctions of MicroRNA-126 in Mice

“…Most members of Caspase family were upregulated in miR-126–deficient eECs (Figure S8B in the Supplemental Material ). Moreover, a toolbox for deducing autophagy status which was built by Bordi et al, 59 had been detected in our integrated single-cell data. Only sixty percentage of genes related to autophagy activation (Induction List) were upregulated after miR-126 knocked out.…”

“…GO analysis identified that top 50 differently expressed genes are mainly related to hypoxia and cell apoptosis. And genes related to apoptosis, including Mex3 family, 58 Caspase family, and a toolbox for deducing autophagy status which was built by Bordi et al, 59 had also been analyzed in single-cell data. As expected, most apoptosis-related genes were upregulated in miR-126–deficient eECs.…”

Tight association of autophagy and cell cycle in leukemia cells

“…As a first step toward a differential characterization of Aut LO , Aut ME , and Aut HI , we conducted gene expression analyses. Although autophagy is basically a cytoplasmic pathway, it can also be subject to transcriptional regulation [ 60 – 62 ]. To examine whether variations in basal autophagy were reflected by differences in the expression of ATG genes, we determined the relative mRNA abundance of two ATG genes that have particularly often shown transcriptional regulation, the LC3B-coding gene MAP1LC3B and ULK1 [ 61 ].…”

Tight association of autophagy and cell cycle in leukemia cells

“…As a rst step toward a differential characterization of Aut LO , Aut ME and Aut HI , we conducted gene expression analyses. Albeit autophagy is basically a cytoplasmic pathway, it can also be subject to transcriptional regulation [59][60][61]. To examine whether variations in basal autophagy were re ected by differences in the expression of ATG genes, we determined the relative mRNA abundance of two ATG genes that have particularly often shown transcriptional regulation, the LC3B-coding gene MAP1LC3B and ULK1 [60].…”