Autophagy is a lysosomal degradation pathway for cytoplasmic material and is activated during cellular stress. Upon induction by a stress signal such as viral infection or amino acid starvation, the first step in autophagy is the formation of an autophagosome. The most published autophagosome marker protein is MAP LC3, which associates to the inner and outer limiting membranes of the autophagosome.

Two forms of LC3 may be seen by Western blot: LC3I which is found in the soluble fraction, and LC3II which is found in the membrane fraction. Both forms are seen in healthy cells, but the proportion of LC3II increases dramatically during autophagy.