The transcriptional and translational landscape of equine torovirus

Hazel Stewart; Katherine Brown; Adam M. Dinan; Nerea Irigoyen; Eric J. Snijder; Andrew E. Firth

infection. The RNA-seq data were analysed to identify genes that were differentially 269 expressed between virus-infected and mock-infected ED cells. We identified 61 270 genes that were upregulated in virus-infected cells; amongst which eight gene 271 ontology (GO) terms were overrepresented, mostly related to the nucleosome or 272 immune responses ( Figure 5 ). We found 24 genes that were downregulated in 273 infected cells, amongst which four GO terms were overrepresented, two of which 274 were related to the ribosome. We also analysed differential translational efficiency 275 (based on the RPF to mRNA ratio) between mock-and virus-infected cells. We 276 identified 22 genes that were translated more efficiently in infected cells; GO 277 analysis indicated that these genes tend to encode proteins that are involved in RNA 278 binding. Only two genes were found to be translated less efficiently in infected cells The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/296996 doi: bioRxiv preprint Two additional proteins are translated from 5' CUG-initiated ORFs. Our initial 283 dataset indicated an excess density of ribosomes translating within the +2/-1 frame 284 upstream of ORF1a and overlapping the 5' end of ORF1a ( Figure 2A ). To further 285 investigate this, we repeated the ribosome profiling using infected cells treated with 286 translation inhibitors prior to flash freezing (harringtonine, HAR, and/or 287 cycloheximide, CHX). HAR specifically arrests initiating ribosomes whilst allowing 288 "run-off" of elongating ribosomes; conversely CHX stalls elongating ribosomes whilst 289 allowing on-going accumulation at initiation sites. Our quality control analysis 290 confirmed the datasets were of similar quality to our previous experiment 291 ( Supplementary Figures 1, 2 and 4) and mapping of the RPFs provided good coverage 292 of the EToV genome ( Figure 6 ). 293