Kinetics and efficiency of polyadenylation of late polyomavirus nuclear RNA: generation of oligomeric polyadenylated RNAs and their processing into mRNA

Gene Regulation and Quality Control in Murine Polyomavirus Infection

Murine polyomavirus (MPyV) infects mouse cells and is highly oncogenic in immunocompromised hosts and in other rodents. Its genome is a small, circular DNA molecule of just over 5000 base pairs and it encodes only seven polypeptides. While seemingly simply organized, this virus has adopted an unusual genome structure and some unusual uses of cellular quality control pathways that, together, allow an amazingly complex and varied pattern of gene regulation. In this review we discuss how MPyV leverages these various pathways to control its life cycle.

How a small DNA virus uses dsRNA but not RNAi to regulate its life cycle

Mouse polyomavirus contains a circular DNA genome, with early and late genes transcribed from opposite strands. At early times after infection, genes encoded from the early transcription unit are predominantly expressed. After the onset of viral DNA replication, expression of genes encoded from the late transcription unit increases dramatically. At late times, late primary transcripts are inefficiently polyadenylated, leading to the generation of multigenomic RNAs that are precursors to mature mRNAs. These transcripts contain sequences complementary to the early RNAs and downregulate early-strand gene expression by inducing RNA editing. Our recent work leads to a model where the production of the multigenomic late RNAs is also controlled by the editing of poly(A) signals, directed by overlapping primary transcripts.

Deletion derivatives of the MuDR regulatory transposon of maize encode antisense transcripts but are not dominant-negative regulators of mutator activities

The maize MuDR/Mu transposable elements are highly aggressive, and their activities are held in check by host developmental and epigenetic mechanisms. The Mutator regulatory element, MuDR, produces both sense and antisense transcripts. We have investigated the impact of the presence of antisense transcripts on the abundance of the corresponding sense messages and on the regulation of Mutator activities. We report that internal deletions in MuDR arise frequently in somatic tissues; preferential loss of the 3' untranslated region of mudrA and/or mudrB containing the intergenic region is correlated with chimeric sense mudrA/antisense mudrB and sense mudrB/antisense mudrA transcripts. Heritable internal deletions are extremely frequent (>10(-2) per element), and the resulting defective MuDR elements also encode antisense transcripts. Expression of endogenous or additional transgene-encoded antisense transcripts neither decreases sense transcript levels nor inhibits Mutator excision activity over the three generations examined. We propose that antisense transcripts produced by MuDR deletions are not dominant-negative regulators of Mutator activities.

Human Ca2+/calmodulin-dependent protein kinase kinase beta gene encodes multiple isoforms that display distinct kinase activity

Ca(+2)/calmodulin-dependent protein kinases (CaMKs) are activated upon binding of Ca(+2)/calmodulin. To gain maximal activity, CaMK I and CaMK IV can be further phosphorylated by an upstream kinase, CaMK kinase (CaMKK). We previously isolated cDNA clones encoding human CaMKK beta isoforms that are heterogeneous in their 3'-sequences (Hsu, L.-S., Tsou, A.-P., Chi, C.-W., Lee, C.-H., and Chen, J.-Y. (1998) J. Biomed. Sci. 5, 141-149). In the present study, we examined the genomic organization and transcription of the human CaMKK beta gene. The human CaMKK beta locus spans more than 40 kilobase pairs and maps to chromosome 12q24.2. It is organized into 18 exons and 17 introns that are flanked by typical splice donor and acceptor sequences. Two major species of transcripts, namely the beta1 (5.6 kilobase pairs) and beta2 (2.9 kilobase pairs), are generated through differential usage of polyadenylation sites located in the last and penultimate exons. Additional forms of CaMKK beta transcripts were also identified that resulted from alternative splicing of the internal exons 14 and/or 16. These isoforms display differential expression patterns in human tissues and tumor-derived cell lines. They also exhibit a distinct ability to undergo autophosphorylation and to phosphorylate the downstream kinases CaMK I and CaMK IV. The differential expression of CaMKK beta isoforms with distinct activity further suggests the complexity of the regulation of the CaMKK/CaMK cascade and an important role for CaMKK in the action of Ca(+2)-mediated cellular responses.

Exon/intron structure and alternative transcripts of the CUTL1 gene

The human CUTL1 gene (Cut-like 1) is a candidate tumor suppressor gene located on chromosome 7 at band 22, a region that is frequently deleted in several human cancers. The gene spans at least 340kb and contains 33 exons. Synthesis of five different transcripts involves two promoter regions, two polyadenylation sites and seven alternative splicing events. The two polyadenylation sites are located at the ends of exons 24 and 33 and are separated by approximately 40kb. Transcription is initiated in two genomic regions, giving rise to alternate first exons which are spliced to a common exon 2. All transcripts contain exons 2 to 14, but differ in their 3' regions. Exon 14 can be spliced alternatively to the beginning or the middle of exon 15, or to exon 25, generating transcripts with exons 15 to 24 or exons 25 to 33. Moreover, exon 16 can be spliced out from the mature transcripts that contain exons 15 to 24. Overall, five distinct transcripts are generated as a result of alternative transcription initiation, splicing and polyadenylation. We discuss potential mechanisms by which alternate polyadenylation site usage may affect alternative splicing events and vice versa.

Epstein-Barr virus latent messages with shuffled leader exons: remnants of circumgenomic transcription?

The EBNA transcription unit which is active in Epstein-Barr virus-immortalized latently infected B lymphocytes covers approximately 60% of the 172-kb genome. Since the genome exists as a circular double-stranded DNA molecule in latently infected cells, it is conceivable that complete copies are made during transcription. Rather than attempt to detect gigantic RNA molecules directly, we used RNA-PCR to detect incorporation of leader exons into mRNA in a shuffled order. The downstream U leader exon was detected spliced upstream of the internal repeat leader exons W1 and W2 in the polyadenylated RNA fraction of spontaneous lymphoblastoid cell lines, restricted phenotype BL cell lines Wanyanyi and Wewak2, and in B95-8, Raji, and Akata cells. Quantitative competitive RNA-PCR showed that the ratio of U exon-containing EBNA1 messages to U exon-shuffled leader messages was approximately 10:1, with large variation from cell line to cell line, and was not affected by induction of the lytic cycle in B95-8, Raji, or Akata cells. Messages with shuffled exons contained only the C2W1 alternative splice, which does not produce an initiator AUG methionine codon for EBNA4 gene expression. The results provide evidence for long-range exon skipping and imply that genome-length transcripts may occur and participate in viral gene expression in latency.

Nuclear antisense RNA. An efficient new method to inhibit gene expression

We describe an efficient new antisense RNA method to inhibit gene expression. Antisense RNAs that are retained in the nucleus bind to target transcripts and appear to lead to the degradation of their targets. Antisense RNAs can be expressed and accumulated specifically in the nucleus if they are not polyadenylated at their 3' ends. In antisense expression vectors we use a cis-acting ribozyme to generate 3'-ends independently of the polyadenylation machinery and thereby inhibit transport of RNA molecules from the nucleus to the cytoplasm. We have evaluated this method in the mouse polyoma virus model system, where nuclear antisense transcripts to the viral early transcription region efficiently reduced the level of viral early-strand RNAs. Nonspecific antisense RNA had no effects on viral gene expression. In comparative studies, nuclear antisense RNAs were significantly more effective in downregulating polyoma virus early RNAs than were conventional antisense molecules, which were processed by polyadenylation.

Stalling by RNA polymerase II in the polyomavirus intergenic region is dependent on functional large T antigen

RNA polymerase II encounters an elongation block and stalls in vivo during transcription of the late strand of polyomavirus DNA. In this study, we performed transcriptional run-on assays and localized the stalling site to a 164-nucleotide region (nt 11-175) that contains specific binding sites for polyomavirus large T antigen. The effect of large T antigen on elongation by RNA polymerase II through this region was examined in cells infected with a mutant polyomavirus (AT3-ts25E) which encodes a thermolabile large T antigen. Removal of functional large T antigen by shifting to the nonpermissive temperature (39 degrees) eliminated stalling by RNA polymerase in this region, although RNA polymerases transcribing other regions of the viral genome were unaffected. RNA polymerase resumed stalling when functional large T antigen was again allowed to accumulate by shifting back to the permissive temperature (32 degrees). We conclude that stalling by RNA polymerase II in vivo is dependent on the presence of functional large T antigen.

A CCAAT box sequence in the adenovirus major late promoter functions as part of an RNA polymerase II termination signal

Termination of transcription by RNA polymerase II has been shown in several cases to require a functional poly(A) addition site, although the actual termination event occurs further downstream. To define in more detail the sequences required for termination, we mapped the site at which transcription terminates on a chimeric plasmid template that contains the adenovirus MLP directing transcription of the SV40 early region. Termination in cells transfected with this plasmid occurs within a discrete promoter-proximal region that contains an inverted CCAAT-box sequence. This region of the MLP was also capable of directing termination, in an orientation-dependent manner, when inserted downstream of the poly(A) site in the plasmid template. In addition, in adenovirus-infected cells, transcription initiated from upstream promoters on the adenovirus chromosome terminates within the same MLP promoter-proximal region, both establishing the physiological relevance of the observed CCAAT-box dependent termination, and also suggesting a possible function for transcription termination in adenovirus infection.

How RNA polymerase II terminates transcription in higher eukaryotes

The termination of transcription of eukaryotic genes by RNA polymerase II, at first sight, appears to be a rather random process, with the heterogeneous transcripts produced being processed to generate their correct 3' ends. However, recent studies have revealed that specific termination or pause sites may influence the process. The mechanism of termination may even play a role in eukaryotic gene regulation.

RNA polymerases stall and/or prematurely terminate nearby both early and late promoters on polyomavirus DNA

Levels of transcription within the E and L strands of the five major PstI fragments of polyomavirus (strain AT3) were measured by pulse-labeling RNA both in infected cells and in isolated nuclei or viral transcription complexes during the late phase of infection. Quantification was assured by hybridization to single-stranded DNAs in solution followed by collection of hybrids on nitrocellulose filters and ribonuclease treatment. The level of in vivo transcription in the region of the early (E strand) promoter was two- to threefold higher than that in all other E-strand regions, suggesting that most RNA polymerases prematurely terminate transcription shortly downstream from this promoter during the late phase. In vitro transcription levels in this region were five- to tenfold higher than in the remainder of the E strand, suggesting that many RNA polymerases 'stall' shortly after initiation in vivo but can be reactivated and continue transcription in vitro upon exposure to detergents and high salt solution. Some premature termination nearby the late (L strand) promoter was also detected by the same method. Strikingly, many RNA polymerases also stalled on the L strand in the region of the early promoter, some 5 x 10(3) bases downstream from the late promoter. Treatment of cells with dichlororibofuranosylbenzimidazole did not affect polymerases that stalled or terminated prematurely, but strongly reduced the presence of polymerases that normally transcribed throughout the entire E or L strand. Examination of the size of RNA chains produced during in vitro incubations showed that many polymerases stalled in vivo within 50 to 100 nucleotides downstream from the initiation sites on both DNA strands. The number of polymerases active in vitro at the E strand promoter was similar to the number of polymerases at the L strand promoter. However, in contrast to L-strand transcription, most of the polymerases that initiated at the E-strand promoter were incapable of extended transcription in vivo. These results suggest that large T antigen-mediated repression of E-strand transcription is not simply due to the exclusion of RNA polymerases from the early promoter. Stalling and/or premature termination by RNA polymerases shortly downstream from the early promoter appears to be a mechanism by which temporal regulation of polyomavirus gene expression can be effected.

3-Methylcholanthrene-induced expression of the cytochrome P-450c gene

Transcriptional control of 3-methylcholanthrene-dependent cytochrome P-450c nuclear RNA induction was directly observed in an in vitro rat liver nuclear transcription system. Mercurated and radiolabeled ribonucleotides were incorporated into nuclear RNA transcribed in vitro, which was then isolated using thiopropyl-Sepharose 6B affinity chromatography. Dot hybridization experiments were carried out using bacteriophage M13 subclones of pRSA57 (a cDNA clone for rat serum albumin), pEB339 (a cDNA clone for rat cytochrome P-450c), and clone 46 (a cDNA clone for mouse cytochrome P1-450). The results of these studies demonstrate that 3-methylcholanthrene does not significantly influence the transcription of the rat serum albumin gene, but does increase the transcription of the cytochrome P-450c gene. Nuclear RNA precursors to the cytochrome P-450c mRNA were characterized by Northern blot analysis. Clone 46 hybridized to nuclear RNA species of 6.7 and 4.0 kb, in addition to the 3.0-kb cytochrome P-450c mRNA. pA8 (a genomic clone for rat cytochrome P-450c), hybridized to the same nuclear RNA species in addition to nuclear RNA species of 4.3, 3.4, and 2.2 kb. M13pd15 (a genomic clone containing information for the first intron of the cytochrome P-450c gene) hybridized to nuclear RNA species of 6.7 and 4.3 kb. All of these nuclear RNA species are polyadenylated. The mRNA coding for cytochrome P-450c was induced maximally in hepatic nuclei at 3 h following 3-methylcholanthrene administration. Maximal accumulation of cytochrome P-450c mRNA in hepatic cytosol has been previously shown to occur at approximately 15 h following 3-methylcholanthrene administration (Bresnick, E., Brosseau, M., Levin, W., Reik, L., Ryan, D. E., and Thomas, P. E. (1981) Proc. Natl. Acad. Sci. USA 78, 4083-4087). These data implicate a possible role of nuclear RNA transport in the regulation of induction of cytochrome P-450c, although further investigations are indicated.