Global Transcriptome Analyses of Cellular and Viral mRNAs during HAdV-C5 Infection Highlight New Aspects of Viral mRNA Biogenesis and Cytoplasmic Viral mRNA Accumulations

Figures

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  Figure 1. The HAdV-C5 transcriptome in A549-infected cells at different time points post-infection. Visualization of total (nuclear and cytoplasmic) mapped sequences across the HAdV-C5 transcriptome at each time point p.i. (A) The annotated transcriptome of HAdV-C5 is shown, represented as green arrows, with each annotated transcript belonging to each of the adenoviral gene families (E1A, E1B, E4, E2A, E2B, and ML (L1–L5)), including the remnants of the E3 region, which is partially deleted in the H5pg4100 virus that was used as “wild-type” HAdV-C5 (see Section 2.1). The directions of arrows represent the coding sequence direction for each viral transcript. Nucleotide position annotations for all transcripts are listed in Table S1. (B–E) Histograms show cumulative coverage of sequencing reads that were mapped to the viral genome at (B) 6, (C) 12, (D) 24, and (E) 48 h p.i. The scale, in total reads, for every histogram is shown on the right.

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  Figure 2. Expression levels of HAdV-C5 mRNAs at early and late time points p.i. Different time points p.i. of (A) total viral mRNA expression values, (B) changes in abundance of the different viral mRNA species produced from each TU, and (C) corresponding proportions of all viral reads. Analyses of changes in abundance of mRNAs and the corresponding relative proportions were performed for individual transcripts of each viral transcription unit: E1A (D,E), E1B (F,G), E2 (H,I), E4 (J,K), and ML (L,M).

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  Figure 3. Cellular cytoplasmic/nucleoplasmic mRNA ratios at different time points post-infection. Cluster heat map of cellular transcripts with FDR-corrected p-values (≤0.05) and fold changes of ≥2. Cytoplasmic-to-nucleoplasmic ratios of cellular mRNAs were z-score transformed and clustered applying the Euclidean distance method. The resulting tree includes three main branches (I–III) and seven clusters (A–G). Blue colors indicate mRNAs with higher cytoplasmic abundance, and mRNAs that are more abundant in the nucleoplasm are represented in the red z-score spectrum. Transcripts associated with each cluster are listed in Table S2.

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  Figure 4. Intracellular distribution of viral and cellular mRNAs at different time points post-infection. All RNAseq reads were assigned to (A) viral and (B) cellular transcripts. Total reads at each time point p.i. are represented as bar graphs. (C) Proportions of cytoplasmic or nucleoplasmic reads are shown for each time point p.i.

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  Figure 5. Viral late mRNAs are comparable in abundance to the most abundant cellular mRNAs in the late phase. Shown is the comparison of the relative abundances of the 35 most abundant cellular mRNAs (green) vs. the viral late mRNAs (blue), at each time point p.i. A detailed list of the cellular top transcripts and their rank in terms of abundance can be found in Table S3.