Fig 2: SARS-CoV-2 infection induces DAXX cytoplasmic re-localization to sites of viral replication.DAXX overexpression restricts SARS-CoV-2. 293T-ACE2 cells were transfected with DAXX WT. 24 h after transfection, cells were infected with the mNeonGreen fluorescent reporter SARS-CoV-2 at the indicated MOI. Cells were either visualized with an EVOS fluorescence microscope (a, b) or stained with an HA-antibody detecting DAXX and imaged by confocal microscopy (c). Scale bars correspond to 200 µm (a) and 30 µm (c). Images shown in (a) were quantified using ImageJ software (b). Data shows the mean ± SD of Fluorescence integrated densities. The analysis was performed on around 200 cells from 3 different fields. Images are representative of 3–6 different fields from 2 independent experiments. d Relocalization of endogenous DAXX during SARS-CoV-2 infection. 293T-ACE2 cells were infected with SARS-CoV-2 at an MOI of 1. 24 h post-infection, cells were labelled with Hoescht and with antibodies against dsRNA (detecting viral RNA, in green) and HA (detecting DAXX, in red). When indicated, the high-resolution Airyscan mode was used. Scale bars correspond to 10 µm for confocal images, and 2 µm for the high-resolution images. Images are representative of 3–6 different fields from 2 independent experiments. Source data are provided as a Source Data file.

Fig 3: DAXX restriction of SARS-CoV-2 is dependent on its chaperone activity but SUMOylation-independent. a Schematic of the DAXX mutants used. The fifteen lysine residues of DAXX 15KR have been mutated to arginine. DAXX?SIM lacks the 732–740 C-terminal residues. Both mutants were described in.48 DAXX?D/E is lacking its 414-505 domain and has been described in52 b, c SUMOylation-deficient DAXX mutants are still able to restrict SARS-CoV-2. 293T-ACE2 cells were transfected with HA-DAXX WT; HA-DAXX 15KR; HA-DAXX?SIM; or with HA-NBR1 as negative control plasmid. 24 h after transfection, cells were infected with SARS-CoV-2 at an MOI of 0.1. When indicated, cells were treated with remdesivir at the time of infection. After 24 h or 48 h, infected cells were double-stained for dsRNA (to read out infection) and HA (to read out transfection efficiency) and acquired by flow cytometry. The percentage of infected cells among HA-positive (transfected) cells for one representative experiment is shown in (b), for the mean ± SD of 3 independent experiments in (c). Statistics: one-way ANOVA using Dunnett’s test, Holm corrected. P values are indicated on the graph. d, e: The chaperone activity of DAXX is required for SARS-CoV-2 restriction. 293T-ACE2 cells were transfected with DAXX WT or with the DAXX?D/E mutant. 24 h after transfection, cells were infected with SARS-CoV-2 mNeonGreen at an MOI of 1. After 24 h, the levels of Spike and GAPDH levels were analyzed by Western Blot (d). A Western Blot representative of 3 independent experiments is shown. In parallel, SARS-CoV-2 replication levels were measured by RT-qPCR targeting the 5' UTR and normalized against RPL13A transcript levels (e). The mean ± SD of 4 independent experiments, with infections carried out in two biological replicates, is represented. Statistics: 1-way ANOVA using Dunnett’s test. P values are indicated on the graph. Source data are provided as a Source Data file.

Fig 4: SARS-CoV-2 PLpro induces the proteasomal degradation of DAXX. a DAXX degradation after infection. 293T-ACE2 cells were infected with SARS-CoV-2 at MOI 0.1. After 24 h, cells were harvested and levels of DAXX, Lamin B, HSP90, Actin, GAPDH, Tubulin, TRIM22, RIG-I and of the viral protein spike were analyzed by Western Blot. A Western Blot representative of 3 independent experiments is shown. b GRL0617 and MG132 treatments restore DAXX expression. 293T-ACE2 cells were infected with SARS-CoV-2 at an MOI of 0.1. When indicated, cells were pretreated 2 h before infection with GRL0617 (at the indicated concentrations), or with MG132 (10 µM), a proteasome inhibitor, or Masitinib (10 µM) a 3CL inhibitor. After 24 h, cells were harvested and levels of DAXX, GAPDH and of the viral protein spike were analyzed by Western Blot. A Western Blot representative of 3 independent experiments is shown. c GRL0617 treatment restores DAXX localization. 293T-ACE2 cells were infected with SARS-CoV-2 at an MOI of 0.1. 24 h post-infection, cells were labelled with Hoescht and with antibodies against dsRNA (detecting viral RNA, in green) and HA (detecting DAXX, in red). When indicated, cells were treated with 50 µM of GRL0617 at the time of infection. Scale bars correspond to 10 µm. Images are representative of 3–6 different fields from 2 independent experiments. d–f: Nsp3 induces DAXX degradation. d 293T-ACE2 cells were transfected with 1 µg of the indicated viral proteins. After 24 h, the levels of DAXX and GAPDH were analyzed by Western Blot. e 293T-ACE2 cells were transfected with the indicated amounts of Nsp3. After 24 h, the levels of DAXX and GAPDH were analyzed by Western Blot. f 293T-ACE2 cells were transfected with 1 µg of Nsp3 or of pcDNA. 6 h post transfection, cells were also, when indicated, treated with 50 µM of GRL0617. Of, 24 h after transfection, the levels of DAXX and GAPDH were analyzed by Western Blot. Western Blots representative from 2 independent experiments are shown. The quantification of band intensity for Fig. 6d–f is shown in Fig. S8b,d, e. Source data are provided as a Source Data file.

Fig 5: DAXX is a restriction factor for SARS-CoV-2. a–c Antiviral activity of ISGs against SARS-CoV-2. A549-ACE2 knocked-out for the indicated genes were generated using a multi-guide approach, leading to pools of KO cells with a high frequency of indels. KO cells were pre-treated with 0 (circles) or 200 (triangles) U/mL of IFNa 24 h prior to infection with SARS-CoV-2 (at an MOI of 0.1). Supernatants were harvested at 72 h p.i. The mean ± SD of three independent experiments, each performed in three biological replicates, is shown. a For the titration of RNA levels, supernatants were heat-inactivated prior to quantification by qRT-PCR. Genome copies/mL were calculated by performing serial dilutions of a synthetic RNA with a known concentration. Statistics: 2-way ANOVA using Dunnett’s test. Significant p values (below 0.05) are indicated on the graph. b For the titration of infectious virus levels by plaque assay, supernatants were serially diluted and used to infect VeroE6 cells. Plaques formed after 3 days of infection were quantified using crystal violet coloration. The limit of detection (LOD) is indicated as a dotted line. Statistics: Dunnett’s test on a linear model, (two-sided). Significant p values (below 0.05) are indicated on the graph. c For each of the indicated KO, the data shown in (a) is represented as fold change in log10 titers (i.e. the log10 titers of the non-treated condition divided by the mean of the triplicate log10 titers IFNa-treated condition, n = 3). Statistics: 2-way ANOVA using Sidak’s test. P values are indicated on the graph (ns: p value > 0.05). d–f Antiviral activity of DAXX against SARS-CoV-2 variants and other viruses. d A549-ACE2 WT or DAXX KO cells were infected at an MOI of 0.1 with the following SARS-CoV-2 strains: Lineage B (original strain); Lineage B.1.1.7. (Alpha variant); Lineage B.1.35.1 (Beta variant); Lineage P1 (Gamma variant). Supernatants were harvested at 72 h p.i. Supernatants were heat-inactivated prior to quantification by qRT-PCR. Genome copies/mL were calculated by performing serial dilutions of a synthetic RNA with a known concentration. The mean ± SD of three independent experiments, with infections carried out in three biological replicates, is shown. Statistics: 2-way ANOVA using Dunnett’s test. Significant p values (below 0.05) are indicated on the graph. e A549-ACE2 WT or DAXX KO cells were infected with Yellow Fever Virus (YFV, Asibi strain, MOI of 0.3) or with Measles Virus (MeV, Schwarz strain expressing GFP, MOI of 0.2). At 24 h p.i., the percentages of cells positive for viral protein E (YFV) or GFP (MeV) was assessed by flow cytometry. The mean ± SD of 3 independent experiments is represented. Statistics: 2-way ANOVA using Sidak’s test. P values are indicated on the graph. f WT or DAXX KO cells were infected at an MOI of 0.1 with SARS-CoV or MERS-CoV. Supernatants were harvested at 72 h p.i. Supernatants were heat inactivated prior to quantification by qRT-PCR. Serial dilutions of a stock of known infectious titer was used as a standard. The mean ± SD of 2 independent experiments, with infections carried out in three biological replicates, is represented. Statistics: 2-way ANOVA using Dunnett’s test. P values are indicated on the graph. Source data are provided as a Source Data file.