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CAGE-seq analysis of Epstein-Barr virus lytic gene transcription: 3 kinetic classes from 2 mechanisms

Fig 2

CAGE-seq readily distinguishes late from early gene transcription start sites (TSS) based on their dependence upon lytic DNA replication and the βγ-encoded vPIC.

CAGE-seq tracks from EBV ΔBALF2, ΔOriLyt, ΔBDLF4, and WT infected HEK293 cells showing TSS location and transcript abundance (in tags per million (TPM)) for A) representative early genes BGLF4 and BGLF5 and B) representative late genes BFRF1 and BFRF3. For each track, the treatment condition is indicated: cells were either uninduced (U), induced by transfection of Rta and Zta (I), or induced by transfection of Rta and Zta, and further trans-complemented with either BALF2 or BDLF4 (I + t) in the appropriate mutant cell line (ΔBALF2 or ΔBDLF4, respectively). In each case, cells were harvested for CAGE-seq 48 hours post-transfection. Scale marker in the WT track indicates track heights depicted in all tracks for the same TSS cluster. * indicates TSS signals surpassing the indicated scale. Full tracks are available to view in an interactive viewer (https://go.wisc.edu/58sxkb).

Fig 2

doi: https://doi.org/10.1371/journal.ppat.1007114.g002