CAGE-seq Analysis of Epstein-Barr virus Lytic Gene Transcription

This study was undertaken to define the EBV genes expressed during viral replication and their dependence upon DNA replication and vPIC. For this work, we employed Cap Analysis of Gene Expression (CAGE-seq) which allows strand-specific quantification of transcription start sites. CAGE-seq avoids cofounding that arises from extensive EBV transcript overlap that limits the ability of RNA-seq (and other conventional high throughput techniques) to quantify individual transcripts. Using this approach with EBV mutants conditional for DNA replication or vPIC activity, we performed a comprehensive characterization of EBV replication gene kinetics indentifying 16 late genes, 32 early genes, and 16 with partial dependence upon DNA replication (leaky late genes).