CMER, an RNA encoded by human cytomegalovirus is most likely transcribed by RNA polymerase III

The properties and functions of virus encoded microRNA, siRNA, and other small noncoding RNAs

microRNAs (miRNAs) represent a class of noncoding RNA species, believed to be regulating gene expression by binding to complementary sites in the 3'UTRs of target mRNAs. They play important regulatory roles in various metabolic pathways in most eukaryotes. The recent discovery of virus encoded miRNAs suggests that viruses may be using them to regulate host and viral gene expression. Another class of closely related small interfering RNAs (siRNAs) also has been found within the HIV-1 genome and shown to be exerting a limited impact on virus reproduction. Additionally, an additional type of viral noncoding RNAs named small noncoding RNAs (sncRNAs) ranging from a few tens to a few hundred nucleotides in length, has also been identified. sncRNAs have a wide phylogenesis and high levels of expression, suggesting they may play an important roles in different species. Here we discuss the genomic organization, expression, conservation as well as potential function of virally encoded miRNA, siRNA, and sncRNAs.

The variable 3' ends of a human cytomegalovirus oriLyt transcript (SRT) overlap an essential, conserved replicator element

The genetically defined human cytomegalovirus (HCMV) lytic-phase replicator, oriLyt, comprises more than 2 kb in a structurally complex region that spans a variety of potential transcription control signals. Several transcripts originate within or cross oriLyt, and we are studying these oriLyt transcription units to determine whether they participate in initiating or regulating lytic-phase DNA synthesis. Results presented here establish the temporal accumulation and structure of the smallest replicator transcript, which we call SRT, and identify a single-sequence element essential to replicator function. SRT was detected as early as 2 h after HCMV infection of human fibroblast cells; transcript levels increased by 24 h and continued to increase thereafter. Consistent with its early appearance, treatment of HCMV-infected cells with the viral DNA polymerase inhibitor phosphonoformic acid had no effect on SRT accumulation; however, no SRT was detected in RNA preparations from cycloheximide-treated infected cells. Additional Northern (RNA) analysis localized the 0.2- to 0.25-kb SRT to an apparently noncoding segment near the center of the oriLyt core region. Reverse transcriptase PCR (rapid amplification of cDNA 5' ends [5'-RACE]) identified a single 5' end. In transient-transfection assays, the sequence immediately upstream of SRT functioned as a promoter responsive to HCMV infection when placed upstream of a reporter gene, suggesting that SRT is the product of a discrete transcription unit. RNA ligase-mediated 3'-RACE showed that SRT is not polyadenylated and has heterogeneous 3' ends within a roughly 45-nucleotide window overlapping an oligopyrimidine sequence having counterparts in the lytic-phase replicators of several herpesviruses. Mutation of the oligopyrimidine element showed that it is essential to oriLyt replicator function; it is the only essential single-sequence HCMV oriLyt replicator element described to date. Collectively, the location of SRT near the center of the oriLyt core region, its early expression, its overlapping relationship with a sequence element essential to replicator function, and its similarities to replicator transcripts in other systems suggest the possibility that SRT plays a role in initiating or regulating HCMV lytic-phase DNA synthesis.

Small RNA expression from the oncogenic region of a highly oncogenic strain of herpesvirus saimiri

Herpesvirus saimiri induces acute lymphomas and leukemias in primates and rabbits. Sequence divergence of the right end unique region of the genome classifies virus strains into three groups (A, B, and C), and previous studies have demonstrated correlation between DNA grouping and oncogenicity. In order to relate different oncogenicity to the underlying molecular mechanisms, we reported earlier the expression of a bicistronic mRNA from the oncogenic region in a highly oncogenic group C strain, and the present study is the first report on small RNA transcripts from the same region. The transcripts and 6.2 kbp on the oncogenic region were sequenced and characterized. We show that four U-type small RNAs are expressed in tumor cells transformed by this strain, in contrast to the seven small RNAs reported from a weakly oncogenic group A strain. Sequence comparisons between the two strains showed that the right end region of strain 484-77 of group C is about 1 kbp shorter. The conserved 5' AUUUA repeats of some small RNAs, and their proposed implication in lymphokine mRNA stabilization, are also discussed.

The divergence between two oncogenic Herpesvirus saimiri strains in a genomic region related to the transforming phenotype

Herpesvirus saimiri strains can be divided into at least three subgroups (A, B, C) based on sequence divergence at the left end of viral unique sequence DNA. Strains of subgroups A and C are highly oncogenic and readily transform simian T-lymphocytes in vitro to interleukin-2 independent growth, while subgroup B strains do not. A left terminal reading frame of a H. saimiri subgroup A strain was shown previously to correlate with the oncogenic phenotype and in vitro transforming potential; the deduced polypeptide was termed STP-A. Furthermore, this same region contains an open reading frame (ORF) for dihydrofolate reductase (DHFR) and genes for five virus-specific U RNAs (HSURs). We now show by sequence analysis of the corresponding region in a subgroup C strain that DHFR and HSUR genes are present in both virus subgroups; however, no sequence homologous to the STP-A reading frame was found in this subgroup C virus. At a position and orientation similar to STP-A, two ORFs were found for peptides sharing a putative transmembrane domain. One of them encodes a peptide with collagen-like repetitions. In addition to the lack of similarity to STP-A, these two reading frames also did not show any similarity to known oncogenes. The organization of sequences at the left junction of unique L- and repetitive H-DNA of H. saimiri suggests frequent recombinational events, possibly accelerating the uptake of foreign genes by the virus.