Transcriptome analysis of lymphoma associated viruses and analysis of viral noncoding RNAs
During the past fifty years, it has become clear that several viruses are etiologically associated with lymphomas. In this research, we performed a global virome survey in 50 lymphoma cell line models using high-throughput RNA sequencing (RNA-seq) data from the Cancer Cell Line Encyclopedia project. This investigation identified EBV, KSHV and HTLV-1 in cell lines already known to harbor these viruses and it identified active infection with the murine retrovirus, MuLV, in two of these cell lines. In depth EBV and KSHV transcriptome analysis led to the discovery of unexpected transcription in several regions of these viral genomes. Through a de novo assembly approach, we solved the genome sequences of the new HTLV-1 and MuLV strains found in the corresponding cell lines. In addition, we developed a computational method to systematically identify and examine all transcribed viral integration sites in virus infected samples. This analysis identified integration sites for EBV, HTLV-1 and MuLV and provided new insights into integration mediated gene disruption and/or activation mechanisms. We also carried out an investigation into EBV lytic transcriptome and identified novel bidirectional transcripts derived from the EBV latent origin of replication, oriP. Both the sense and antisense oriP transcripts (oriPtRs and oriPtLs) were expressed with the kinetics of late viral genes and predominantly localized in the nucleus. Structure modeling showed that both oriPtRs and oriPtLs can form stable hairpin structures that were found to be hyper-edited by the adenosine deaminase, ADAR1. These transcripts were associated with the nuclear paraspeckle component, NonO. oriPtL overexpression reduced the mRNA levels of several heat shock proteins and globally enhanced EBV gene expression. oriPtL knockdown inhibited EBV production and global EBV gene expression and influenced the expression of several immune regulatory genes. These results indicate that oriPtL may have multiple functions in EBV self- regulation and in modulating cellular environment. In sum, this research provides an atlas of the virome and virus transcriptome in 50 lymphoma cell line models and it sheds light into the functions of novel non-coding RNAs transcribed from the oriP region during EBV reactivation.