Inferred transcription factors mediating host cell chromatin accessibility changes.

In (A) we show the response to T. gondii infection in the human genome is marked by increased accessibility of chromatin at numerous loci. The results in (B) describe the motifs enriched in these loci that open their chromatin, corresponding to the binding sites of three known TFs. The results in (C) show the numbers of expressed genes containing one or more of the TF binding site motifs within 5 kb of their transcription start site. For those genes with only one motif, testing their ontological properties in (D) revealed the common property of induction of immune responses, but also other properties that are likely to be more favorable to the pathogen.</p

A model derived from genomic assay data for the host cellular response to <i>T</i>. <i>gondii</i> infection.

By inferring the TFs mediating the host cell response, we can further predict the cell signaling pathways induced by T. gondii infection in human fibroblasts. How the known GRA24 induction of p38 MAPK signaling influences the transcriptional response remains uncertain, and we include the possibility that T. gondii TFs may contribute to host cell transcriptional dysregulation.</p

Project overview and host gene transcriptional response to <i>T</i>. <i>gondii</i> infection.

We show in (A) the overview of the experiments performed, depicting the in vitro infection of human fibroblasts with T. gondii, with transcriptional (RNA-seq) and chromatin accessibility (ATAC-seq) studies performed before and 24 hours after infection, and alignment of the reads obtained to both the human and T. gondii genomes. The RNA-seq results in (B) show more human genes upregulated (yellow) than downregulated (blue) with infection, with ADAMTS15 strongly upregulated. Using network analysis, we extracted genes interacting with ADAMTS15 (C) and showed that other metalloproteases were upregulated with infection (D). (E-G) show the major groups of gene ontologies in the remaining upregulated genes.</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

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

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