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

Figure 5. lncRNA3 generates a stable non poly adenylated intron.

(A) RNA-seq reads aligned to the negative strand of lncRNA3 locus in both HHV-6A and HHV-6B are presented. Thin gray lines represent spliced reads, blue lines represent reads aligned to either the exons or intron, pink lines represent reads that span the first exon intron junction. In regions with very high coverage (>100 reads per 50 nt region) reads were downsampled so that maximum 100 reads per region are displayed. Gray bars represent the total reads coverage without omissions. (B) RT-qPCR measurements of the HHV-6A and HHV-6B lncRNA3 intron RNA. Values were normalized to the HHV-6 U21 gene. cDNA was prepared with either oligo-dT or random hexamers primers and the ratio of these measurements is presented. Error bars represent standard error of biological duplicates. P-values were calculated using Student's t-test. * p-value<0.05 and ** p-value<0.01.

Figure 5.

Figure 5—figure supplement 1. Abundance of lncRNA stable intron in total RNA.

Figure 5—figure supplement 1.

Normalized RNA abundance as measured by RNA-seq of total RNA (without poly-A selection) from cells infected for 72 hr with (A) HHV-6B or (B) HCMV, of (A) the spliced lncRNA3 and the stable intron, or (B) the spliced RNA5.0 and the stable intron. Error bars represent standard error of biological replicates in A and triplicates in B. (C) Northern blot analysis of total RNA extracted from HHV-6B infected Molt-3 cells at 72hpi with probes against the lncRNA3 intron.