RNASeq of infected HFFs.

Differential gene analysis and interaction analysis of human-aligned transcripts. IFNγ treatment is denoted as yes or no. For the interaction analysis, sheet names represent the IFNγ effect for the first strain relative to the IFNγ effect for the second strain (i.e., WT|IFN_vs_dGRA57|IFN represents +IFNγ vs -IFNγ in the RHΔKu80 group relative to +IFNγ vs -IFNγ in the RHΔGRA57 group). (XLSX)</p

Antibodies used for immunofluoresence assays.

Toxoplasma gondii secretes protein effectors to subvert the human immune system sufficiently to establish a chronic infection. Relative to murine infections, little is known about which parasite effectors disarm human immune responses. Here, we used targeted CRISPR screening to identify secreted protein effectors required for parasite survival in IFNγ-activated human cells. Independent screens were carried out using 2 Toxoplasma strains that differ in virulence in mice, leading to the identification of effectors required for survival in IFNγ-activated human cells. We identify the secreted protein GRA57 and 2 other proteins, GRA70 and GRA71, that together form a complex which enhances the ability of parasites to persist in IFNγ-activated human foreskin fibroblasts (HFFs). Components of the protein machinery required for export of Toxoplasma proteins into the host cell were also found to be important for parasite resistance to IFNγ in human cells, but these export components function independently of the identified protein complex. Host-mediated ubiquitination of the parasite vacuole has previously been associated with increased parasite clearance from human cells, but we find that vacuoles from GRA57, GRA70, and GRA71 knockout strains are surprisingly less ubiquitinated by the host cell. We hypothesise that this is likely a secondary consequence of deletion of the complex, unlinked to the IFNγ resistance mediated by these effectors.</div

Opera Phenix image acquisition parameters and Harmony analysis sequence used for automated ubiquitin recruitment analysis.

Opera Phenix image acquisition parameters and Harmony analysis sequence used for automated ubiquitin recruitment analysis.</p

Retention of the Native Epigenome in Purified Mammalian Chromatin

<div><p>A protocol is presented for the isolation of native mammalian chromatin as fibers of 25–250 nucleosomes under conditions that preserve the natural epigenetic signature. The material is composed almost exclusively of histones and DNA and conforms to the structure expected by electron microscopy. All sequences probed for were retained, indicating that the material is representative of the majority of the genome. DNA methylation marks and histone marks resembled the patterns observed in vivo. Importantly, nucleosome positions also remained largely unchanged, except on CpG islands, where nucleosomes were found to be unstable. The technical challenges of reconstituting biochemical reactions with native mammalian chromatin are discussed.</p></div

Deletion of GRA57, GRA70, or GRA71 leads to reduced host ubiquitin recruitment to the PVM.

(A) Schematic of automated high-content imaging analysis pipeline to determine ubiquitin recruitment levels. (B, C) Recruitment of total host ubiquitin (FK2) to Toxoplasma vacuoles in (B) HFFs and (C) MEFs. Host cells were pre-stimulated with 100 U/ml IFNγ for 24 h, infected with indicated lines for 3 h prior to fixation and staining for total ubiquitin. Recruitment of ubiquitin was automatically counted using high-content imaging and analysis. (D) Recruitment of total ubiquitin (FK2), K63-linked ubiquitin, linear ubiquitin (M1), and the E3 ligase RNF213 to Toxoplasma vacuoles. HFFs were pre-stimulated with 100 U/ml IFNγ for 24 h, infected with indicated lines for 3 h prior to fixation and staining. Recruitment was automatically quantified for FK2, M1, and RNF213. K63 recruitment was manually scored, with minimum 100 vacuoles scored per condition. p-Values were calculated by paired two-sided t test. *, p p p p S9 Data. HFF, human foreskin fibroblast; MEF, mouse embryonic fibroblast; PVM, parasitophorous vacuole membrane.</p

Inhibition of parasite egress in the first 3 h of infection does not restore ubiquitination or survival of ΔGRA57 vacuoles.

(A) Recruitment of total ubiquitin to Toxoplasma vacuoles at 3 h postinfection, with the addition of 5 μm Compound 2 at 30 min postinfection to inhibit parasite egress. HFFs were pre-stimulated with 100 U/ml IFNγ for 24 h, infected with indicated lines for 30 min prior to addition of Compound 2. HFFs were fixed at 3 h postinfection and stained for total ubiquitin. Recruitment was automatically counted using high-content imaging and analysis. (B) Parasite survival in IFNγ-stimulated HFFs at 3 h postinfection, with the addition of 5 μm Compound 2 at 30 min postinfection to inhibit parasite egress. Parasite numbers were quantified through automated high-content imaging, with survival calculated as the percentage of intracellular parasites in IFNγ-stimulated cells relative to the total in unstimulated cells. p-Values were calculated by paired two-sided t test. *, p p p p S10 Data. (TIF)</p

Raw data for Cytation plate reader IFNγ survival assays.

(A) HFFs, (B) MEFs, and (C) HFFs +/− tryptophan supplementation. Total mCherry area +/− IFNγ per biological replicate. (XLSX)</p

Loss of GC-rich nucleosomes during purification.

<p>(A) Normalized read counts for nucleosomes extracted from nuclei or from purified genomic chromatin digested to mononucleosomes, averaged around all TSS’s. Note greater depletion around the TSS in the purified material than in the nuclei. (B) Nucleosome loss after purification as a function of nucleosomal GC content. Nucleosome read counts from nuclei and purified chromatin were counted in 500 bp windows across the genome. The log2 ratio of the two is displayed. The grey line shows a fitted Loess function, and the dashed line shows the average genomic GC content of 41%. (C) Normalized read counts averaged around all CpG islands (CGI).</p

Survival of ΔGRA57 parasites is not rescued with exogenous supplementation of tryptophan.

HFF IFNγ restriction assays as in Fig 2, with the addition of 1 mM L-tryptophan to treated conditions simultaneous with IFNγ pre-stimulation. Untreated controls had 0.1 N NaOH added as a vehicle control. Host cells were infected in technical triplicate with the indicated parasite strains for 24 h at an MOI of 0.3, and then imaged live on a Cytation 5 plate reader. Total mCherry signal area per well was measured to determine parasite growth in IFNγ stimulated relative to unstimulated cells. Data displayed as mean survival + standard deviation from 2 biological replicates. Source data can be found in S3 Data. (TIF)</p

Mass spectrometry analysis of genomic chromatin.

<p>Mass spectrometry analysis of genomic chromatin.</p