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

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

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

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

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

Chromatin accessibility profiles in the <i>T</i>. <i>gondii</i> genome indicate incomplete annotations of genes.

The chromatin accessibility pattern at all of the ATAC-seq peaks in the T. gondii genome at the tachyzoite stage of its life cycle is shown in (A). When the subset within ±5 kb of annotated T. gondii transcription start sites (TSS) is plotted with the associated genes represented to the right of the TSS (B, blue line), the patterns shows a skewing relative to the distributions of all peaks from panel (A) (gray distribution). Examples of genes are show to represent how the annotated TSS can be several kilobases (kb) from the upstream ATAC-seq peak and the start of the RNA-seq reads, with examples of 1.53 kb (C) and 4.03 kb (D) differences illustrated. In (E) we gain the additional insight that the two annotated genes are only associated with a single upstream ATAC-seq peak, indicating that there is only one transcript at this locus and the genes could be combined into a single annotation.</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