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Cited by 65Autophagy in Disease and TherapyUbiquitin and proteasome pathwaysCalcium signaling and nucleotide metabolism

Detection of WIPI1 mRNA as an indicator of autophagosome formation

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Tsuyuki, Satoshi, Takabayashi, Mei, Kawazu, Manami, Kudo, Kousei, Watanabe, Akari, Nagata, Yoshiki, Kusama, Yusuke, Yoshida, Kenichi·2014·Autophagy
DOI 10.4161/auto.27419PMC PMC4077887
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Abstract

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.

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  • The authors identified 20 targets related to autophagy activation and validated them by qPCR: ATG10, ATG14, ATG16L1, ATG3, ATG4, ATG7, ATG9A, BCL2, GABARAP, GABARAPL1, MAP1LC3B, NBR1, OPTN, PINK1, SQSTM1, ULK1, ULK2, UVRAG, WDR45, WIPI1.

    “In a first case, starting from experimental data available in the literature, we identified 20 targets related to autophagy activation and validated them by qPCR: ATG10, ATG14, ATG16L1, ATG3, ATG4, ATG7, ATG9A, BCL2, GABARAP, GABARAPL1, MAP1LC3B, NBR1, OPTN, PINK1, SQSTM1, ULK1, ULK2, UVRAG, WDR45, WIPI1 (Fig. 2) [18–27].”

    From A gene toolbox for monitoring autophagy transcription (2021) · cites this paper as [26]

  • The activation list was derived from comparison of publications reporting conditions of gene up-regulation upon autophagy activation.

    “A so called “activation list” has been derived from the comparison of publications, in which we reported conditions of gene up-regulation upon autophagy activation [18–27].”

    From A gene toolbox for monitoring autophagy transcription (2021) · cites this paper as [26]

  • The restricted "induction list" for the prediction of autophagy activation state is made of 20 targets and was obtained by combining data from previous publications documenting increased mRNA expression following autophagy induction.

    “The restricted “induction list” for the prediction of autophagy activation state, made by 20 targets, was obtained combining data from previous publications [18–27], in which have been documented the increase of the mRNA expression following autophagy induction.”

    From A gene toolbox for monitoring autophagy transcription (2021) · cites this paper as [26]

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Authors
Tsuyuki, S., Takabayashi, M., Kawazu, M., Kudo, K., Watanabe, A., Nagata, Y., Kusama, Y., & Yoshida, K.
Affiliations
Meiji University (JP)
Corresponding author
Yoshida, Kenichi
ORCID
Yoshida, Kenichi
Venue
Autophagy
Publisher
Informa UK Limited
Published
2013-12-23
Volume
10
Issue
3
Pages
497-513
ISSN
  • 1554-8627 (ISSN-L)
  • 1554-8635
DOI
10.4161/auto.27419
PMC
PMC4077887
OpenAlex
W2075761732
Cited by
65
References
0
Citations by year
2026: 1 · 2025: 1 · 2024: 3 · 2023: 15 · 2022: 4 · 2021: 7 · 2020: 6 · 2019: 4 · 2018: 6 · 2017: 6 · 2016: 4 · 2015: 5 · 2014: 3
FWCI
2.92
Type
journal article
Language
en
Open access
Locations
  • Autophagy (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
Meiji University
Topics
  • Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Physiology › Calcium signaling and nucleotide metabolism
Keywords
WIPI1, autophagosome formation, autophagy-related genes, LC3B, transcriptional regulation, thapsigargin, C2-ceramide, amino acid starvation, rapamycin, autophagy markers, RNA interference, HeLa cells, A549 cells
MeSH terms
Autophagy-Related Proteins, Autophagy, Carrier Proteins, Cell Line, HeLa Cells, Humans, Membrane Proteins, Microtubule-Associated Proteins, Phagosomes, RNA, Messenger, Gene Expression, Sirolimus, RNA Stability

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