Abundant 5 kb RNA of Human Cytomegalovirus without a Major Translational Reading Frame

Abstract

SUMMARYAlthough all herpesviruses are similar in their temporal regulation of gene expression, the organization of the immediate early (IE) genes varies markedly between the different members of the group. Most of the IE transcripts of human cytomegalovirus originate from a restricted region within the long unique segment of its linear dsDNA genome of 235 kb. One of the predominant transcripts from the IE region is a 5 kb RNA. Northern blot analyses revealed that this class of RNA is continuously present in infected cells. It was detected at high levels in IE and late RNA preparations, and in low amounts in early RNA preparations. It was not confined to the poly(A) + fraction upon oligo(dT) selection, but also appeared in similar amounts in poly(A)-fractions. Fine mapping of this transcript was done by nuclease protection and primer extension. The RNA appeared to be unspliced, and no signals such as TATA or CCAAT, known to be important elements in eukaryotic RNA polymerase II promoters, were found close to the 5' end. Sequence analysis revealed multiple stop codons throughout the AT-rich potential coding region. Since no splicing was found to occur, the largest protein deduced from the DNA sequence would be of not more than 12000 Mr. However, a computer program designed to detect protein-coding DNA sequences by codon usage did not reveal significant evidence for a protein encoded in this region. Therefore this RNA is likely to represent an unprecedented case of a large non-coding transcript present in cells that are lytically infected by an animal virus.

Discrete Clusters of Virus-Encoded MicroRNAs Are Associated with Complementary Strands of the Genome and the 7.2-Kilobase Stable Intron in Murine Cytomegalovirus

“…It remains to be seen whether the spatial relationship between miRNAs and stable introns is a common feature in viruses and what role this plays in pathogenesis. However, the MCMV stable intron is orthologous to the HCMV stable intron (20,39), and miRNAs have not previously been cloned in its vicinity.…”

Unravelling the interaction of human cytomegalovirus with dendritic cells by using SuperSAGE

“…Supernatants containing the amplified RNA were collected, digested with DNase I and precipitated, yielding 26.9 and 24.9 mg amplified RNA (uninfected and HCMV-infected samples, respectively). Although the majority of viral mRNA is polyadenylated and will be detected by this method, viral transcripts without polyadenylation also exist (Plachter et al, 1988;Mach et al, 1989;Adair et al, 2004).…”

In vivo and in vitro analysis of transcriptional activation mediated by the human cytomegalovirus major immediate-early proteins.

“…Like other members of the herpesvirus family, the genome of HCMV is temporally expressed during the viral life cycle (16,56,81,88,89). The (16,17,29,33,34,56,64,79,80,82,88,89,91). At least three IE RNAs have been found to be transcribed from these regions (Fig.…”