Translational profiling of B cells infected with the Epstein-Barr virus reveals 5’ leader ribosome recruitment through upstream open reading frames

The Epstein-Barr virus (EBV) genome encodes several hundred transcripts. Using total RNA sequencing and ribosome profiling, we have characterized the transcriptional and translational scope of B cells infected with EBV. We could show that viral transcripts are translated at variable efficiency and that several viral genes show ribosome recruitment to the 5’ leader region of mRNAs. We used two different virus strains with differing in vitro characteristics to study EBV translation and could show that in cells infected with the weakly replicating EBV strain some lytic genes showed evidence of monosomal ribosome recruitment mainly in the 5’ leader region and on start codons in the absence of protein production. Finally, we could identify 25 novel upstream open reading frames that potentially regulate the translation efficiency of some viral genes. Sample 1 experimental set-up: B cells were infected with either the B95-8 or M81 Epstein-Barr virus (EBV) strain. These cells were then treated with cycloheximide for 10 min and ribosome profiles were generated that were then converted into a cDNA library for sequencing. In parallel, these cells were also treated for 2 minutes with harringtonine and again ribosome profiles were generated that were subsequently sequenced. Additionally, the total RNA was sequenced from cells infected with the B95-8 or M81 strain. Sample 2 experimental set-up: B cells were infected with either the B95-8 or M81 EBV strain. These cells were treated for 2 or 5 minutes with harringtonine and ribosome profiles were generated that were subsequently sequenced. Additionally, the total RNA from cells infected with the B95-8 or M81 strain was sequenced. HEK293 cells carrying a stably transfected B95-8 BACMID were induced into lytic replication by transfecting a lytic cycle transactivator and these cells were then treated for 2 minutes with harringtonine. Ribosome profiling was also performed with this sample and it was subsequently sequenced.