High Risk HPVs do not encode canonical microRNAs (original) (raw)

2018

Abstract

(A) Coverage plots of miDGE DNA-seq and small RNA-seq across the genomes of HPV18 and HPV17. Filled green plots at the top of each panel show DNA-seq coverage, the three plots underneath show mapped small RNA-seq from: PV: HEK293T-cells transfected with our papillomavirus miDGE library, PV filtered: same reads as in PV, but filtered to eliminate low-complexity reads JMRV: Serving as a negative control, derived from 293T-cells transfected with our JMRV miDGE library. JMRV read counts were normalized to correct for different sequencing depths between PV and JMRV miDGE experiments (see total read counts in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1007156#ppat.1007156.t001" target="_blank">Table 1</a>). Asterisk indicates a previously purported miRNA candidate region suggested in the literature [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1007156#ppat.1007156.ref039" target="_blank">39</a>], which is nonspecific (detected in the negative control JMRV miDGE analysis, lower plot) and can be eliminated by removing low complexity reads (center plot). (B) RNA-seq coverage for the most abundantly mapped HPV in 303 tumors in the TCGA CESC project [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1007156#ppat.1007156.ref050" target="_blank">50</a>]. Each of the 303 libraries are represented on the X-axis (sorted based on Y-axis value). Y-axis indicates the percentage of the positions in the HPV genome with read mappings. Libraries with > = 50% coverage (213 libraries) were used for subsequent analysis. (C) Percentages of TCGA cervical squamous cell carcinoma (CESC) libraries with miRDeep2 miRNA identifications for each set of reference sequences. Number of libraries examined is 213. (D) Number of unique miRDeep2 miRNA identifications across TCGA CESC libraries for each set of reference sequences. Number of libraries examined is 213. (E) Percentages of Qian et al. [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1007156#ppat.1007156.ref040" target="_blank">40</a>] libraries with miRDeep2 miRNA identifications for each set of reference sequences. Number of libraries examined is 12. (F) Number of unique miRDeep2 miRNA identifications across Qian et al. libraries for each set of reference sequences. Number of libraries examined is 12. (G) Raw read counts of all small RNAs mapping to the indicated reference sequences for each library from Qian et al.</p

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