We show examples of loci where the motifs enriched at <i>T</i>. <i>gondii</i> loci of open chromatin are also found in the host genome at sites that open chromatin during <i>T</i>. <i>gondii</i> infection, representing candidate loci where <i>T</i>. <i>gondii</i> TFs may be acting directly on host chromatin.

(TIF)</p

The candidate transcription factor binding site motifs from Fig 6 were used to identify loci in the host human genome where these motifs are present and chromatin becomes accessible during infection, defining candidate loci where <i>T</i>. <i>gondii</i> transcription factors may be directly acting on the host human genome.

We list the 46 candidate loci and the associated motifs. (XLSX)</p

S6 Fig -

The expected nucleosomal periodicity pattern of chromatin is revealed from the insert size plots of panel (A), representing the reads aligning to the T. gondii nuclear genome, whereas in (B) we see no evidence for such nucleosomal organization in reads mapping to the T. gondii apicoplast DNA. (TIF)</p

ATAC-seq sequencing data metrics for the human and <i>T</i>. <i>gondii</i> genomes.

(XLSX)</p

Inference of transcription factor binding motifs in the <i>T</i>. <i>gondii</i> genome.

Analysis of the loci of open chromatin in the T. gondii genome reveals enrichment for several motifs (A). The purine (AG)-rich motif is the most abundantly represented at T. gondii promoters (B) followed by the known AP2 motif (GCATGCA), with the TATA-containing motif in 25.1% of promoters. Panel (C) shows the properties of the subset of genes with the AP2 motif at their promoters.</p

The detailed expression data for the ME49 reference genome annotated genes.

We present a raw counts file with data for each replicate, and the normalized counts file on which our analyses were based. (XLSX)</p

S3 Fig -

The location of ATAC-seq peaks (left) and differentially-accessible regions (DARs, right) relative to annotated transcription start sites (TSS) in the human genome. Whereas ATAC-seq peaks are strongly enriched at TSS, only 51 (9.6%) of DARs are located within 5 kb of annotated transcription start sites (yellow shading). (TIF)</p

S5 Fig -

In (A) we show the number of RNA-seq reads from T. gondii to be consistently greater than 2 million in all replicates. In (B) we illustrate how most genes in the T. gondii genome are represented consistently across replicates, also showing this quantitatively in the UpSet plot of panel (C). (TIF)</p