An siRNA screen for ATG protein depletion reveals the extent of the unconventional functions of the autophagy proteome in virus replication

Mauthe, Mario; Langereis, Martijn; Jung, Jennifer; Zhou, Xingdong; Jones, Alex; Omta, Wienand; Tooze, Sharon A.; Stork, Björn; Paludan, Søren Riis; Ahola, Tero; Egan, Dave; Behrends, Christian; Mokry, Michal; de Haan, Cornelis; van Kuppeveld, Frank; Reggiori, Fulvio

U2OS (a gift from G. Strous, University Medical Center Utrecht, Utrecht, Netherlands), HeLa-mCeaCam1, HEK-mCeaCam1 , HEK293T-REx, HA-Flag-ATG13 and HA-Flag-FIP200 (Behrends et al., 2010; Jung et al., 2015) , BGM kidney, baby hamster kidney 21 (BHK-21) and HeLa cells, and immortalized ATG13 −/− mouse embryonic fibroblasts (MEFs; a gift from X. Wang, National Institute of Biological Science, Beijing, China) retrovirally transformed Figure 10 . RNA sequencing provides insight into the unconventional function(s) of ATG13 and FIP200. U2OS cells depleted of ATG13, ATG7, or FIP200, or treated with control siRNA, were infected or not with CV for 7 h at MOI 1. RNA sequencing was performed on isolated RNA as described in Materials and methods. (A) Venn diagrams showing upand down-regulated genes in ATG13-and FIP200-depleted cells, whose expression was not altered in ATG7 knockdown cells. The overlapping areas indicate genes that are differentially expressed in both ATG13-and FIP200-depleted cells. Genes whose transcription is also altered in ATG7depleted cells were not considered, because their differential expression is very likely linked to one or more functions of autophagy. (B) Gene Ontology analysis of the genes that were differentially and specifically expressed in ATG13-and FIP200-depleted cells, exposed or not to CV. (C) Schematic model for the autophagy-dependent and -independent functions of ATG13 and FIP200.