Fig 4.

(A) Read coverage across the LMP1 locus illustrates the lytic LMP1 transcript structure in induced Akata cells and the classic type III latency LMP1 transcript structure in JY cells. The y axis is the number of reads spanning each genomic coordinate (x axis). Thick lines represent coding sequences, medium thickness lines represent untranslated regions, and thin lines with leftward arrows represent introns. Red values are the number of reads that span the indicated junctions. Coverage data were derived from Novoalign, and junction evidence was taken from TopHat. (B) Quantitative RT-PCR was used to determine the ratio of transcripts spanning exon 2 to exon 3 versus exon 1 to 2 in cytoplasmic fractions from uninduced or induced Akata cells and the type III latency cell lines JY, Jijoye, and X50-7.