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. 2014 Jan 16;10(1):e1003847. doi: 10.1371/journal.ppat.1003847

Figure 4. mRNA-Seq reveals ribosome-protected non-coding RNAs in KSHV.

Figure 4

(A) The PAN transcript is protected by ribosomes during the lytic cycle. mRNA-Seq and Ribo-Seq of the PAN gene at 48 hr post reactivation. Ribo-Seq in cells treated with CHX (blue) or Harr (teal) show the accumulation of ribosomes on three distinct coding regions of this transcript. (B) PAN codes for three putative sORFs, PAN1.1 (37aa), PAN1.2 (44aa), and PAN1.3 (25aa), which can be identified as ribosome-populated regions (in capital letters). The predicted signal peptide in PAN1.1 is underlined. (C) The K5/K6 antisense transcript is devoid of nucleosomes following lytic reactivation. mRNA-Seq and Ribo-Seq of the genomic region from 24200 bp to 29700 bp at 48 hr post induction. The light blue solid line corresponds to the K5/K6 antisense RNA. Solid black arrows indicate transcripts and grey arrowheads indicate coding regions. (D) Northern blot for the same region depicted in (C). The A and B probes are indicated as short broken lines in (C). PFA: phosphonoformate. See also Figure S5 and Table S3.