biostudies-literatureUnknown13Han CIn <i>Saccharomyces cerevisiae</i>, Atg1 is a core autophagy-related (Atg) protein kinase (PK) in regulating macroautophagy/autophagy, by physically interacting with numerous other proteins, or by phosphorylating various substrates. It is unclear how many Atg1-interacting partners and substrates are also involved in regulating autophagy. Here, we conducted transcriptomic, proteomic and phosphoproteomic profiling of Atg1-dependent molecular landscapes during nitrogen starvation-triggered autophagy, and detected 244, 245 and 217 genes to be affected by <i>ATG1</i> in the autophagic process at mRNA, protein, and phosphorylation levels, respectively. Based on the Atg1 interactome, we developed a novel artificial intelligence (AI) framework, inference of autophagy regulators from multi-omic datFrontiers in cell and developmental biology1554958https://www.ebi.ac.uk/biostudies/studies/S-EPMC12069372biostudies-literatureOmic AI reveals new autophagy regulators from the Atg1 interactome in &lt;i&gt;Saccharomyces cerevisiae&lt;/i&gt;.PMC12069372Fu SFeng ZZhang JTang DXue YZhang WXiao LPeng DYi CChen YGou YHan CLiu DZhang CfalseOmic AI reveals new autophagy regulators from the Atg1 interactome in &lt;i&gt;Saccharomyces cerevisiae&lt;/i&gt;.In <i>Saccharomyces cerevisiae</i>, Atg1 is a core autophagy-related (Atg) protein kinase (PK) in regulating macroautophagy/autophagy, by physically interacting with numerous other proteins, or by phosphorylating various substrates. It is unclear how many Atg1-interacting partners and substrates are also involved in regulating autophagy. Here, we conducted transcriptomic, proteomic and phosphoproteomic profiling of Atg1-dependent molecular landscapes during nitrogen starvation-triggered autophagy, and detected 244, 245 and 217 genes to be affected by <i>ATG1</i> in the autophagic process at mRNA, protein, and phosphorylation levels, respectively. Based on the Atg1 interactome, we developed a novel artificial intelligence (AI) framework, inference of autophagy regulators from multi-omic dat2025-01-01T00:00:00Z20252026-04-18T03:15:45.252Z2026-04-18T03:11:03.788ZS-EPMC120693724036502110.3389/fcell.2025.1554958