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. 2020 Jan 16;9:e50960. doi: 10.7554/eLife.50960

Figure 4. Identification of three highly abundant and conserved viral long non-coding RNAs (lncRNAs).

Viral transcripts that appear to be lncRNAs are shown as purple rectangles. Reads from RNA-seq are presented in green and reads containing polyA are presented in blue. The ribosome profiling (CHX), Harringtonine (Harr) and lactimidomycin (LTM) profiles are presented in red. (A) A transcript initiating within the origin of replication. One putative ORF not detected by our predictions (see Figure 6) is shown as a striped blue rectangle. (B) A spliced transcript initiating between U17 and U18. (C) Three possible isoforms of a spliced transcript with alternative splicing, initiation and termination, as well as a putative stable intron.

Figure 4—source data 1. RNA-seq and CHX Ribo-seq read density of previously annotated ORFs and novel lncRNAs for HHV-6A and HHV-6B.

Figure 4.

Figure 4—figure supplement 1. Conservation by synteny of newly discovered HHV-6 lncRNAs.

Figure 4—figure supplement 1.

(A and B) Reads from RNA-seq are presented in green. Black rectangles mark canonical ORFs and purple rectangles mark the putative lncRNAs (A) a lncRNA initiating within the lytic origin of replication of HHV-6A, HHV-6B and HCMV (RNA4.9). (B) A spliced lncRNA, likely generating a stable intron, transcribed from the locus between the viral helicase gene and a conserved early phosphoprotein gene in HHV-6A, HHV-6B, HCMV and Murine CMV (MCMV).
Figure 4—figure supplement 2. RNA abundance of canonical ORFs and viral lncRNAs is conserved between HHV-6A and HHV-6B.

Figure 4—figure supplement 2.

Scatter plot of normalized RNA expression levels of canonical HHV-6 ORFs and novel lncRNAs. Gray dots represent ORFs, colored dots represent lncRNAs (lncRNA1 in red, lncRNA2 in green and lncRNA3 in blue).