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Figure 3 | Retrovirology

Figure 3

From: Tailored enrichment strategy detects low abundant small noncoding RNAs in HIV-1 infected cells

Figure 3

Alignment and characterization of identified sncRNAs. (A) 216 unique sncRNAs from nine libraries (Supplementary dataset 1) were aligned to the reference strain HIV-1HXB2 and cluster in 67 contigs distributed throughout the whole genome of HIV-1. The coverage of sncRNA per nucleotide, the single unique clones (black: sense HIV-1 sncRNAs, pink: antisense HIV-1 sncRNAs), and the contig numbers are shown. (B) The length (nucleotides, nt) distribution of all unique HIV-1 sncRNAs is depicted. Sense sncRNAs are shown in black, antisense sncRNAs are shown in pink. (C) Probing the influence of target molecule length on hybridization efficacy, libraries F, G, H, and J underwent a second size separation step before undergoing a second round of hybridization enrichment. Dehybridized cDNA was separated into two fractions of 80-110 bp or 50-80 bp length and both probed separately for hybridization efficacy. Green full circles denote HIV-1 derived sncRNAs, black open circles denote non-HIV-1 sncRNAs. Both fractions successfully retrieved sncRNA in the second round hybridization. 20-25 nucleotide long sncRNAs were retrieved from both fractions and comprised 40.1% of all sncRNAs in the small size fraction and 11.1% in the large size fraction (p < 0.0001, Chi square test). (D) Pie chart depicting the distribution of different human cellular sncRNAs in all libraries.

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