Table 1.

Methods for the analysis of autophagy progression in yeast and mammalian cells.

	Yeast	Mammals
1. Induction and nucleation
A. Induction
Nutrient deprivation	X	X
Rapamycin	X	X
B. Inhibition
Pharmacological	X^a	X
Genetic	X	X^b
C. Assessment
Electron microscopy	X	X
PAS localization	X
Atg13/ATG13 dephosphorylation	X	X
Atg1/ULK1 kinase activity	X	X
Upregulation of ATG gene expression	X	X
2. Expansion and maturation
A. Assessment
GFP-Atg8/LC3	X	X
Protease protection/sequestration assays	X	X
TAKA assay	X
Atg4/ATG4 protease activity	X	X
3. Fusion
A. Inhibition
Pharmacological	X^a	X
Genetic	X	X^b
B. Assessment
Electron microscopy	X	X
Fluorescence microscopy	X	X
Immunoblot (GFP processing)	X	X^c
Pho8Δ	X
4. Degradation and efflux
A. Inhibition
Pharmacological	X^a	X
Genetic	X	X^b
B. Assessment
Electron microscopy: autophagic body accumulation	X
Fluorescence microscopy	X	X
Radioactive efflux	X	X
Assay for new protein synthesis	X	X
Long-lived protein degradation	X	X

Although autophagy can be inhibited pharmacologically in yeast, it is more typical to use genetic methods such as null or conditional mutants.

Traditionally this has been done with RNAi, but now can also be achieved with Cas9 CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology.

The ability to detect GFP-LC3 processing is is cell type-dependent.