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Our appreciation for the extent of Epstein Barr virus (EBV) transcriptome complexity continues to grow through findings of EBV encoded microRNAs, new long non-coding RNAs as well as the more recent discovery of over a hundred new polyadenylated lytic transcripts. Here we report an additional layer to the EBV transcriptome through the identification of a repertoire of latent and lytic viral circular RNAs. Utilizing RNase R-sequencing with cell models representing latency types I, II, and III, we identified EBV encoded circular RNAs expressed from the latency Cp promoter involving backsplicing from the W1 and W2 exons to the C1 exon, from the EBNA BamHI U fragment exon, and from the latency long non-coding RPMS1 locus. In addition, we identified circular RNAs expressed during reactivation including backsplicing from exon 8 to exon 2 of the LMP2 gene and a highly expressed circular RNA derived from intra-exonic backsplicing within the BHLF1 gene. While expression of most of these circular RNAs was found to depend on the EBV transcriptional program utilized and the transcription levels of the associated loci, expression of LMP2 exon 8 to exon 2 circular RNA was found to be cell model specific. Altogether we identified over 30 unique EBV circRNAs candidates and we validated and determined the structural features, expression profiles and nuclear/cytoplasmic distributions of several predominant and notable viral circRNAs. Further, we show that two of the EBV circular RNAs derived from the RPMS1 locus are detected in EBV positive clinical stomach cancer specimens. This study increases the known EBV latency and lytic transcriptome repertoires to include viral circular RNAs and it provides an essential foundation and resource for investigations into the functions and roles of this new class of EBV transcripts in EBV biology and diseases. [ABSTRACT FROM AUTHOR]

Recent studies have shown the contribution of miRNAs to cancer pathogenesis. Prostate cancer is the most commonly diagnosed cancer in men. Unlike other major types of cancer, no single gene has been identified as being mutated in the majority of prostate tumors. This implies that the expression profiling of genes, including the non-coding miRNAs, may substantially vary across individual cases of this cancer. The within-class variability makes it possible to reconstruct or infer disease-specific miRNA-mRNA correlation and regulatory modular networks using high-dimensional microarray data of prostate tumor samples. Furthermore, since miRNAs and tumor suppressor genes are usually tissue specific, miRNA-mRNA modules could potentially differ between primary prostate cancer (PPC) and metastatic prostate cancer (MPC). We herein performed an in silico analysis to explore the miRNA-mRNA correlation network modules in the two tumor subtypes. Our analysis identified 5 miRNA-mRNA module pairs (MPs) for PPC and MPC, respectively. Each MP includes one positiveconnection (correlation) module and one negative-connection (correlation) module. The number of miRNAs or mRNAs (genes) in each module varies from 2 to 8 or from 6 to 622. The modules discovered for PPC are more informative than those for MPC in terms of the implicated biological insights. In particular, one negative-connection module in PPC fits well with the popularly recognized miRNA-mediated post-transcriptional regulation theory. That is, the 3'UTR sequences of the involved mRNAs (∼620) are enriched with the target site motifs of the 7 modular miRNAs, has-miR-106b, -191, -19b, -92a, - 92b, -93, and -141. About 330 GO terms and KEGG pathways, including TGF-beta signaling pathway that maintains tissue homeostasis and plays a crucial role in the suppression of the proliferation of cancer cells, are over-represented (adj.p<0.05) in the modular gene list. These computationally identified modules provide remarkable biological evidence for the interference of miRNAs in the development of prostate cancers and warrant additional follow-up in independent laboratory studies. [ABSTRACT FROM AUTHOR]

Epstein-Barr virus (EBV) reactivation involves the ordered induction of approximately 90 viral genes that participate in the generation of infectious virions. Using strand-specific RNA-seq to assess the EBV transcriptome during reactivation, we found extensive bidirectional transcription extending across nearly the entire genome. In contrast, only 4% of the EBV genome is currently bidirectionally annotated. Most of the newly identified transcribed regions show little evidence of coding potential, supporting noncoding roles for most of these RNAs. Based on previous cellular long noncoding RNA size calculations, we estimate that there are likely hundreds more EBV genes expressed during reactivation than was previously known. Limited 5= and 3= rapid amplification of cDNA ends (RACE) experiments and findings of novel splicing events by RNA-seq suggest that the complexity of the viral genome during reactivation may be even greater. Further analysis of antisense transcripts at some of the EBV latency gene loci showed that they are "late" genes, they are nuclear, and they tend to localize in areas of the nucleus where others find newly synthesized viral genomes. This raises the possibility that these transcripts perform functions such as new genome processing, stabilization, organization, etc. The finding of a significantly more complex EBV transcriptome during reactivation changes our view of the viral production process from one that is facilitated and regulated almost entirely by previously identified viral proteins to a process that also involves the contribution of a wide array of virus encoded noncoding RNAs. [ABSTRACT FROM AUTHOR]

Abstract: The Epstein–Barr virus (EBV) is associated with lymphoid and epithelial cancers. Initial EBV infection alters lymphocyte gene expression, inducing cellular proliferation and differentiation as the virus transitions through consecutive latency transcription programs. Cellular microRNAs (miRNAs) are important regulators of signaling pathways and are implicated in carcinogenesis. The extent to which EBV exploits cellular miRNAs is unknown. Using micro-array analysis and quantitative PCR, we demonstrate differential expression of cellular miRNAs in type III versus type I EBV latency including elevated expression of miR-21, miR-23a, miR-24, miR-27a, miR-34a, miR-146a and b, and miR-155. In contrast, miR-28 expression was found to be lower in type III latency. The EBV-mediated regulation of cellular miRNAs may contribute to EBV signaling and associated cancers. [Copyright &y& Elsevier]