The length but not the sequence of the polyoma virus late leader exon is important for both late RNA splicing and stability

Adami, Guy R.; Carmichael, Gordon G.

doi:10.1093/nar/15.6.2593

Cited by 22 publications

(25 citation statements)

References 50 publications

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“…Cytoplasmic RNA made from this construct was compared with wild-type RNA in an RNase protection assay which detected early spliced species (as an internal control for transfection efficiencies and RNA amounts) and late Vispliced species. Such an assay has been reported in other work from our laboratory (4,7). The results are shown in Fig.…”

supporting

confidence: 69%

“…1 In the 1-13 and I-11 lanes the upper band is intermediate in size from that representing two tandem Li exons (lane [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16] or two tandem L2 exons (lane Py), indicating that the shorter Li had spliced to wild-type-length L2. Thus, Li and L2 exons can splice to each other in long primary transcripts, with a terminal splice to a body exon.…”

mentioning

confidence: 99%

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Splice site choice in a complex transcription unit containing multiple inefficient polyadenylation signals.

Luo

Carmichael

1991

Mol. Cell. Biol.

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The relationship between polyadenylation and splicing was investigated in a model system consisting of two tandem but nonidentical polyomavirus late transcription units. This model system exploits the polyomavirus late transcription termination and polyadenylation signals, which are sufficiently weak to allow the production of many multigenome-length primary transcripts with repeating introns, exons, and poly(A) sites. This double-genome construct contains exons of two types, those bordered by 3' and 5' splice sites (Li and L2) and those bordered by a 3' splice site and a poly(A) site (Vi and V2 In a number of recent studies involving different systems, evidence has been presented that alternate poly(A) site selection can be associated with different 3' splice site choices (5,21,22,29,38; see references 39, 42, and 53 for reviews). These studies have most often been done with complex transcription units which have multiple exons, introns, and poly(A) signals. In such systems, alternative pathways of pre-mRNA processing involve either cell-specific (9, 10, 21) or temporal (23, 42, 52) regulation of poly(A) site or splice site selection. One example of cell-specific regulation is the switch between secreted and membrane forms of the immunoglobulin M heavy chain. Studies have suggested that this switch is regulated at the level of poly(A) site choice (21,29,34,41,49). Thus, in the immunoglobulin M system, choice of alternative poly(A) signals may lead to altered splicing pathways. Some recent results, however, have been inconsistent with such a model of poly(A) site dominance and have instead suggested that there may be competition between splicing and polyadenylation (44, 45). In contrast, the expression of calcitonin and the calcitoningene related peptide, also controlled in a cell-specific manner from a complex transcription unit containing two poly(A) sites, clearly appears to be regulated at the step of splice site recognition, which in turn leads to the use of the nearest downstream poly(A) signal (10,22,38).An example of temporal regulation of pre-mRNA processing occurs in the human adenovirus major late transcription unit (8, 42, 52). At different times after infection, different mRNA species arising from the same transcriptional promoter are seen. Late in infection there are five distinct late mRNA families (8,23,25,52). Each family contains three to seven mRNAs, due to the use of different 3' splice sites (12,19,42), and each family is associated with the use of a * Corresponding author. different late poly(A) site (Li to L5). This differs from early in infection, when only the Li poly(A) site is used efficiently (8, 52).We have studied the relationship between splice site and poly(A) site choice in a model system based on the polyomavirus late transcription unit. Like the systems described above, polyomavirus late primary transcripts are complex, with pre-mRNA processing involving the choice of alternative splice sites and poly(A) sites. The major difference between this system and others is that the pol...

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confidence: 69%

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confidence: 99%

Splice site choice in a complex transcription unit containing multiple inefficient polyadenylation signals.

Luo

Carmichael

1991

Mol. Cell. Biol.

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“…Previous results from our laboratory have shown that mutations that destabilize the late-strand transcripts result in increased expression of the early-strand RNAs (28,55,56). An example of this antisense-induced regulation is shown in Fig.…”

Section: Resultsmentioning

confidence: 93%

Nuclear antisense RNA induces extensive adenosine modifications and nuclear retention of target transcripts

Kumar

Carmichael

1997

Proc. Natl. Acad. Sci. U.S.A.

182

148

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Antisense RNA may regulate the expression of a number of eukaryotic genes, but little is known about its prevalence or mechanism of action. We have used a model system in which antisense control can be studied both genetically and biochemically. Late in polyoma virus infection, early-strand mRNA levels are down-regulated by nuclear antisense RNA from the late strand. Analysis of early-strand transcripts isolated late in infection revealed extensive base modifications. In many transcripts almost half of the adenosines were altered to inosines or guanosines. These results suggest modification of RNA duplexes by double-stranded RNA adenosine deaminase or a related enzyme. Probes that detect only modified RNAs revealed that these molecules are not highly unstable, but accumulate within the nucleus and are thus inert for gene expression. Antisense-induced modifications can account for most or all of the observed regulation, with the lowered levels of early-strand RNAs commonly observed late in infection resulting from the fact that many transcripts are invisible to standard hybridization probes. This work suggests that similar antisense-mediated control mechanisms may also operate under physiological conditions in uninfected eukaryotic cells, and leads to the proposal that there is a novel pool of nuclear RNAs that cannot be seen with many molecular probes heretofore used.

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“…A polyadenylated subset is processed by leader to leader splicing, generating mature transcripts with a single mRNA body sequence, and multiple copies of a 57-nt leader (3,5,10,13,28,32,34,38,44). Leader-to-leader splicing, and hence the synthesis of giant late transcripts, plays an important role in the generation of a stable mature 16S VP1 mRNA (4,5). The exact fate and role of the early giant RNA remain to be determined.…”

Section: Discussionmentioning

confidence: 99%

Kinetic Analysis of the Steps of the Polyomavirus Lytic Cycle

Chen

Fluck

2001

J Virol

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Kinetic studies of the accumulation of early and late transcripts, early and late proteins, genomes, and live virus, during the lytic cycle of murine polyomavirus wild-type A2, were carried out in synchronized NIH 3T3 cells released from G 0 by the addition of serum after infection. This first-time simultaneous analysis of all parameters of the virus life cycle led to new insights concerning the transcriptional control at the early-to-late transition. During the early phase, early transcripts were synthesized at very low levels, detectable only by reverse transcription-PCR, from 6 h postinfection (hpi). Large T protein could be detected by 8 hpi (while infected cells were in the G 1 phase). The level of expression of the middle T and small T proteins was lower than that of large T at all times, due, at least in part, to a splicing preference for the large-T 5 splice site at nucleotide 411. A large increase in the level of both early and late transcripts coincided closely with the detection in mid-S phase of viral genome amplification. Thereafter, both classes of transcripts continued to further accumulate up to the end of the experiments (48 hpi). In addition, during the late phase, "giant" multigenomic transcripts were synthesized from the early as well as the late promoter. Thus, a major type of transcriptional control appears to be applied similarly to the transcription of both early and late genes. This view differs from that in the literature, which highlights the enhancement of late transcription and the repression of early transcription. However, despite this parallel transcriptional control, additional regulations are applied which result in higher levels of late compared to early transcripts, as previously described. In the accompanying article, a key role for middle T and/or small T in this late-phase enhancement of early and late transcription is demonstrated (16). Other novel findings, e.g., the synthesis of a very abundant short early promoter proximal RNA, are also described.Polyomaviruses have served as important model systems for the understanding of various aspects of cellular organization and function, such as chromatin structure, the role of enhancers in gene expression, splicing mechanism, and the composition of the DNA replication machinery, to name a few. This is in part a consequence of the DNA nature and small size of the genomes of this virus family, which render viral replication highly dependent on, and hence compatible with, cellular processes. As a result, and with the added interest in their capacity to induce neoplastic transformation, these viruses have been the subjects of extensive studies.Surprisingly at this late stage of analysis, there has been no comprehensive study of the temporal relationships between all the various steps of the lytic cycle. Current references to the timing of these steps invariably quote the 1981 review by Acheson (2), which offers a thorough integration of the studies available at the time. However, these studies were done at different times, in differ...

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The length but not the sequence of the polyoma virus late leader exon is important for both late RNA splicing and stability

Cited by 22 publications

References 50 publications

Splice site choice in a complex transcription unit containing multiple inefficient polyadenylation signals.

Splice site choice in a complex transcription unit containing multiple inefficient polyadenylation signals.

Nuclear antisense RNA induces extensive adenosine modifications and nuclear retention of target transcripts

Kinetic Analysis of the Steps of the Polyomavirus Lytic Cycle

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