Identification and characterization of short leader and trailer RNAs synthesized by the Ebola virus RNA polymerase
Fig 2
RNA-Seq analysis of (A) small RNAs (<200 nt) or (B) poly(A) RNAs derived from EBOV-infected HuH7 cells. (A) Length of EBOV leader transcripts in small RNA libraries. The vast majority of reads had their 5’-end at position 2, thus a 55-meric leaderRNA had its 3’-end at the TSS (position 56); leaderRNA reads with lengths between 15 and 100 nt were were defined as viral leader transcripts and used as read pool for leaderRNA length/3’-end analysis. Error bars represent standard errors of the mean (SEM) calculated for each transcript length based on three biological replicates (S3 Table). Dashed vertical lines demarcate arbitrary length windows, with percentages indicated; the antigenomic leader and part of the 5’-UTR of the NP mRNA are shown schematically below the graph. (B) Analysis of NP mRNA reads with 5’-ends between antigenome position 54 and 70 (% of reads at each position). The dashed vertical line marks the annotated EBOV transcription start site (TSS). Error bars indicate SEM based on three biological replicates (S3 Table). The sketch at the bottom shows the genomic 3’-leader with the expected transcription start site at nt 56 (light blue arrow). The RNA-Seq analysis is consistent with position 56 being the major TSS, but left the possibility open that some transcripts may be initiated at position 57 and 58 in EBOV-infected cells.