Detection of WIPI1 mRNA as an indicator of autophagosome formation

Autophagy. 2014 Mar;10(3):497-513. doi: 10.4161/auto.27419. Epub 2013 Dec 23.


Autophagy is a cellular bulk degradation system for long-lived proteins and organelles that operates during nutrient starvation and is thus a type of recycling system. In recent years, a series of mammalian orthologs of yeast autophagy-related (ATG) genes have been identified; however, the importance of the transcriptional regulation of ATG genes underlying autophagosome formation is poorly understood. In this study, we identified several ATG genes, including the genes ULK1, MAP1LC3B, GABARAPL1, ATG13, WIPI1, and WDR45/WIPI4, with elevated mRNA levels in thapsigargin-, C2-ceramide-, and rapamycin-treated as well as amino acid-depleted HeLa cells except for MAP1LC3B mRNA in rapamycin-treated HeLa cells. Rapamycin had a weaker effect on the expressions of ATG genes. The increase in WIPI1 and MAP1LC3B mRNA was induced prior to the accumulation of the autophagy marker protein MAP1LC3 in the thapsigargin- and C2-ceramide-treated A549 cells. By counting the puncta marked with MAP1LC3B in HeLa cells treated with different autophagy inducers, we revealed that the time-dependent mRNA elevation of a specific set of ATG genes was similar to that of autophagosome accumulation. The transcriptional attenuation of WIPI1 mRNA using RNA interference inhibited the puncta number in thapsigargin-treated HeLa cells. Remarkably, increases in the abundance of WIPI1 mRNA were also manifested in thapsigargin- and C2-ceramide-treated human fibroblasts (WI-38 and TIG-1), human cancer cells (U-2 OS, Saos-2, and MCF7), and rodent fibroblasts (Rat-1). Taken together, these results suggest that the detection of WIPI1 mRNA is likely to be a convenient method of monitoring autophagosome formation in a wide range of cell types.

Keywords: MAP1LC3B; WIPI1; autophagosome; autophagy; biomarker; gene expression; mRNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Autophagy / genetics*
  • Autophagy / physiology
  • Autophagy-Related Proteins
  • Carrier Proteins / genetics*
  • Cell Line
  • Gene Expression
  • HeLa Cells
  • Humans
  • Membrane Proteins / genetics*
  • Microtubule-Associated Proteins / genetics*
  • Microtubule-Associated Proteins / metabolism
  • Phagosomes / genetics
  • Phagosomes / metabolism*
  • RNA Stability / physiology
  • RNA, Messenger / metabolism*
  • Sirolimus / pharmacology*


  • Autophagy-Related Proteins
  • Carrier Proteins
  • Membrane Proteins
  • Microtubule-Associated Proteins
  • RNA, Messenger
  • WIPI-1 protein, human
  • Sirolimus