Mapping the spliced and unspliced late lytic SV40 RNAs

A cDNA cloning vector that permits expression of cDNA inserts in mammalian cells

This paper describes a plasmid vector for cloning cDNAs in Escherichia coli; the same vector also promotes expression of the cDNA segment in mammalian cells. Simian virus 40 (SV40)-derived DNA segments are arrayed in the pcD vector to permit transcription, splicing, and polyadenylation of the cloned cDNA segment. A DNA fragment containing both the SV40 early region promoter and two introns normally used to splice the virus 16S and 19S late mRNAs is placed upstream of the cDNA cloning site to ensure transcription and splicing of the cDNA transcripts. An SV40 late region polyadenylation sequence occurs downstream of the cDNA cloning site, so that the cDNA transcript acquires a polyadenylated 3' end. By using pcD-alpha-globin cDNA as a model, we confirmed that the alpha-globin transcript produced in transfected cells is initiated correctly, spliced at either of the two introns, and polyadenylated either at the site coded in the cDNA segment or at the distal SV40 polyadenylation signal. A cDNA clone library constructed with mRNA from SV40-transformed human fibroblasts and this vector (about 1.4 X 10(6) clones) yielded full-length cDNA clones that express hypoxanthine-guanine phosphoribosyltransferase (Jolly et al., Proc. Natl. Acad. Sci. U.S.A., in press).

Analysis in Cos-1 cells of processing and polyadenylation signals by using derivatives of the herpes simplex virus type 1 thymidine kinase gene

Bal31 nuclease was used to resect the herpes simplex virus type 1 thymidine kinase (tk) gene from its 3' end, and a plasmid, pTK206, was isolated that lacked the processing and polyadenylation signals normally found at the 3' end of the gene. The wild-type gene, pTK2, and pTK206 were each transferred to pSV010, a plasmid containing the simian virus 40 (SV40) origin of DNA replication, allowing replication and analysis of the patterns of transcription in Cos-1 cells. Fragments of DNA containing processing and polyadenylation signals from SV40 and polyoma virus were inserted into the 3' end of the resected tk gene, pTK206. We found that tk gene expression requires a processing and polyadenylation signal, that signals from SV40 and polyoma virus could substitute for the herpes simplex virus tk signal, and that considerable differences in the levels of tk mRNA were present in Cos-1 cells transfected by these gene constructs. In addition, tk gene expression was restored to a low level after the insertion of an 88-base-pair fragment from the middle of the SV40 early region. Processing and polyadenylation do not occur in the vicinity of this fragment in SV40, even though it contains the hexanucleotide 5'-AAUAAA-3'.

Post-transcriptional processing of simian virus 40 late transcripts in injected frog oocytes

The capacity of fully grown Xenopus oocytes to process messenger RNA precursors has been assessed using transcripts synthesized from simian virus 40 (SV40) DNA microinjected into the oocyte nucleus. In oocytes, stable transcripts of the SV40 virion protein genes have undergone at least four post-transcriptional maturation steps: cleavage at 3' splice sites, formation of a mature 3' terminus, addition of poly(A), and selective intracellular partitioning, such that only those RNAs with a mature 3' terminus and poly(A) are located in the cytoplasm. Apparently unspliced transcripts with mature 3' termini are transported into the oocyte cytoplasm. A prominent transcript of roughly the full length of SV40 DNA, bearing a 5' terminus in the same region as late mRNA and confined to the nucleus, is found in oocytes injected with SV40 DNA. The possibility that this transcript may serve as a precursor to late mRNA is discussed.

A simian virus 40-encoded protein of Mr 74,000 daltons is structurally related to the capsid proteins of the virus

We have demonstrated the synthesis of a 74,000-dalton protein (74K protein) in African green monkey kidney cells infected with simian virus (SV)40. The 74K protein was detected late during the lytic cycle. Its synthesis was inhibited by arabinosyl cytosine as was the synthesis of the capsid proteins. Monospecific antibodies raised against VP1 and VP3 precipitated the structural proteins and the 74K protein. The 74K protein was not found in purified virions. Tryptic peptide analysis demonstrated that the 74K protein shares methionine- and serine-containing peptides with VP1 and VP3 and thus is structurally related to the capsid proteins.

Site-specific base substitution and deletion mutations that enhance or suppress transcription of the SV40 major late RNA

Transcriptional analysis of SV40 late promoter mutants indicates that the DNA sequence 5'-GGTACCTAACC-3' (map positions 294-304) is important in the control of SV40 late RNA expression. C to T base substitutions at map positions 298, 299 and 304 increased initiation of late RNA synthesis at map position 325 five to ten fold. G to A base substitutions at map positions 294 and 295 decreased RNA initiation by a factor of 2 to 3. Deletion of nucleotides 295-298 reduced RNA initiation by a factor of 4 to 5. S1 analysis of in vivo RNA, isolated 24-36 hr after infection, demonstrated that the four base deletion not only decreased RNA initiation at nucleotide 325, but also increased RNA initiation at three alternate sites located approximately 125 nucleotides upstream from the major late RNA initiation site.

Altered utilization of splice sites and 5' termini in late RNAs produced by leader region mutants of simian virus 40

We compared the 5' termini and splices of the late 16S and 19S RNAs synthesized by wild-type simian virus 40 and five mutants containing deletions in their late leader region. All mutants produced more unspliced 19S RNA than did wild-type virus, and in two mutants, unspliced 19S RNA constituted more than 60% of the total 19S species. The other three mutants each utilized predominantly a different one of the three spliced species of 19S mRNA. All mutants also produced decreased quantities of 16S mRNA, indicating that they may be defective for splicing both late RNAs. None of the 5' termini of the 16S and 19S RNAs made by the five mutants predominated as in those made by the wild type. Some of the mutant 5' termini were the same as those used by the wild type, whereas others were different. Although present, the major 5'-end positions used by the wild type were frequently not used as major sites by the mutants. In addition, mutants with very similar deletion endpoints synthesized RNAs with different 5' ends. Thus, downstream mutations have a pronounced effect on the location of 5' ends of the late RNAs, and there is no obvious involvement of a measuring function in the placement of 5' ends. For all mutants and wild-type virus, the 5' termini used for 16S and 19S RNAs showed major differences, with some degree of correlation found between the 5' ends and the internal splices of specific mRNA species. A model for the regulation of simian virus 40 late gene expression is presented to explain these findings.

The sequence of 3'-termini of mRNAs from early region III of adenovirus 2

The cloned cDNA sequences corresponding to early region III transcripts (76.6-86.0 map units) of adenovirus 2 were analyzed with a view to determine the structure of their 3'-termini. The clones pE7, pE22 and pE34, which contain a part of or the entire coding sequence for the Mr 19000 glycoprotein, showed microheterogeneity with respect to the poly(A) addition site, with the polyadenylation occurring 17, 26, or 29 nucleotides downstream from the hexanucleotide, 5'-ATTAAA-3'. The clone pE17 which represents a copy of the mRNA ending at 86.0 map units showed the presence of the sequence 5'-AATAAA-3', 16 nucleotides before the poly(A) tail.

Polyoma virus early and late mRNAs in productively infected mouse 3T6 cells

We mapped polyoma virus-specific mRNAs isolated from productively infected mouse 3T6 cells on the viral genome by analyzing nuclease S1-resistant RNA-DNA hybrids. The polyoma early mRNAs, which code for the three T antigens, have several 5' ends near 73 map units (m.u.). During the late phase of infection an additional 5' end is found near 71 m.u. All of the major early mRNAs have common 3' ends at 26.01 m.u. There is a minor species of early mRNA with a 3' end at 99.05 m.u. There are two proximal and two distal splice junctions in the early region which are used to generate three different spliced early mRNAs. There are three late mRNAs encoding the three virion proteins, VP1, VP2, and VP3. The late mRNAs have common 3' ends at 25.34 m.u. The late mRNAs have heterogeneous 5' leader sequences derived from the region between 65.53 and 68.42 m.u. The leader sequences are joined to the bodies of the messages coding for VP2, VP3, and VP1 at 66.59, 59.62, and 48.57 m.u., respectively. These results confirm and extend previous analyses of the fine structure of polyoma mRNAs.

Methylation of simian virus 40 Hpa II site affects late, but not early, viral gene expression

DNA methylation has been correlated with reduced gene expression in a number of studies, although evidence for a casual link between the two events has been lacking. Because microinjection of simian virus 40 (SV40) DNA into the nucleus of Xenopus laevis oocytes results in the synthesis of both early and late viral gene products, it was possible to test whether a specific methylation event can affect gene expression. The single SV40 Hpa II site at 0.72 SV40 map units was specifically methylated with Hpa II methylase. When this DNA was injected into oocytes, there was a marked reduction in the synthesis of the major late viral capsid protein VP-1, relative to the synthesis by an unmethylated control. However, production of the early proteins (the large and small tumor antigens) was not affected by Hpa II methylation. Therefore, methylation at a single site on the viral DNA located near the 5' end of the late region can specifically repress late gene expression. The possible mechanisms by which this repression is mediated are discussed.

Hybrid selection of small RNAs by using simian virus 40 DNA: evidence that the simian virus 40-associated small RNA is synthesized by specific cleavage from large viral transcripts

The simian virus 40 (SV40)-associated small RNA (SAS-RNA), approximately 64 nucleotides, is virally encoded within a region of the viral late (+) DNA strand which encodes no known protein. The SAS-RNA arises in abundance late in SV40 lytic infection. Previous data indicate that the synthesis of the SAS-RNA may be under the control of the normal late viral promoter; i.e., inhibition of transcription from the late promoter results in cessation of SAS-RNA synthesis. The synthesis of SAS-RNA was examined to determine whether the SAS-RNA is the product of cleavage from noncoding regions of nuclear late transcripts or an independent transcription product like 5S RNA, or the adenovirus VA-RNAs. The data described below suggest that SAS-RNA is cleaved from large late transcripts. In vitro transcription of DNA fragments containing the SAS-RNA coding region yielded no SAS-RNA synthesis; this result was supported by DNA sequence analysis, which indicated no promoter-like regions either within or flanking the SAS-RNA coding region. In support of a cleavage mechanism, the SAS-RNA has a 3'-phosphate end, an occurrence which is indicative of nuclease cleavage. In addition, 5'-end labeling of the SAS-RNA was possible only after calf alkaline phosphatase treatment; this indicates that the SAS-RNA is not capped. Hybrid selection analysis was used to demonstrate that separation of the SAS-RNA coding region from the normal late promoter resulted in elimination of SAS-RNA synthesis. This was demonstrated in SV40-transformed cells in which integration of a single copy of SV40 breaks the continuity of the late coding region, so that the SAS-RNA coding region is physically separated from the normal late promoter. The lack of SAS-RNA synthesis indicates that the SAS-RNA coding region cannot function as a primary transcription unit. The same result and conclusion were obtained by using a permissive cell line transformed by SV40 (COS-1 cells); here it was found that the integrated SAS-RNA coding region was not expressed even during a viable lytic infection in which the SAS-RNA could be expressed from the infecting viral genomes. The simplest conclusion drawn from the data is that the SAS-RNA is cleaved from larger late transcripts which initiate at the normal late promoter. This conclusion suggests that many of the small RNAs found in normal eucaryotic cells may be synthesized by specific cleavage rather than by primary transcription. In the course of these studies several small cellular RNAs were detected, due to their specific hybrid selection, by using SV40 DNA. Primary mapping and characterization data of these RNAs are also presented.

Variety in the level of gene control in eukaryotic cells

In light of present progress in the understanding of how messenger RNA is constructed in eukaryotic cells, the levels of gene control are discussed. Transcriptional control, assessed by the rate of synthesis of specific nuclear RNA, is strongly indicated to be the most frequent level of control. Definition of eukaryotic transcription units as simple (encoding one protein) and complex (encoding two or more proteins) affords a framework in which to discuss control at the level of RNA processing for which several examples also are known. Finally, differential stability of cytoplasmic mRNAs and differential translation, both well established, are briefly described.

Evidence for simian virus 40 late transcriptional control: mixed infections of wild-type simian virus 40 and a late leader deletion mutant exhibit trans effects on late viral RNA synthesis

Mixed infections involving equal multiplicities of wild-type simian virus 40 and viable deletion mutant dl861 resulted in decreased cytoplasmic levels of wild-type-derived male mRNA, as well as very low to undetectable levels of mutant-derived late mRNA, as compared with individual infections. The dl861 deletion removes 16 to 25 base pairs from the late leader region. This deletion was shown to be the direct cause of the mixed-infection effect; replacement of the deletion with wild-type sequences restored normal levels of late mRNAs in mixed infections. Other viral functions, e.g., early gene expression and replication, were found to be unaffected by the dl861 deletion. Further examination of the mixed-infection effect showed that the levels of unspliced nuclear precursors of late mRNA, derived from both the mutant and wild-type genomes, were decreased or undetectable, in accord with the cytoplasmic results. Thus, the effect appears to be occurring at the transcriptional level. These data demonstrate a trans-acting effect on late transcription, which is detectable due to the presence of the dl861 mutant in the mixed infection. This finding is indicative of a diffusible factor which exerts a control on simian virus 40 late gene expression at the transcriptional level. A model for positive control of simian virus 40 late gene expression is presented.

Simian virus 40-rabbit beta-globin recombinants lacking late mRNA splice sites express cytoplasmic RNAs with altered structures

Deletions were introduced at exon-intron boundaries in the late region of a simian virus 40-beta-globin cDNA recombinant to study the role of splicing in the formation of simian virus 40 late cytoplasmic RNAs. The recombinant was used as a wild type because it allowed characterization of mutant RNAs expressed from defective genomes in the presence of comparable RNAs contributed by the coinfecting helper virus. Removal of a 17-base pair segment at map position 0.76, which included a portion of the leader sequence implicated in the splicing of the major 16S mRNA, prevented expression of 16S-type mRNA. The same mutant accumulated cytoplasmic 19S-type mRNA, but the assortment of the 5' ends of these mRNAs differed from the assortment of the wild-type counterparts. Another mutant that lacks nucleotide sequences implicated in the splicing of the major 16S mRNA and one of the principal 19S-type RNAs accumulated a 16S-type mRNA with a previously undetected leader splice, and assortment of 19S mRNAs with new or normally underrepresented splices, and even a species of unspliced cytoplasmic 19S mRNA.

Simian virus 40 mutant with transposed T-antigen and VP1 genes

A simian virus 40 mutant with the T-antigen gene transposed to the late region of the viral genome has been constructed. This transposed molecule directed the synthesis of a full-sized, 92,000-dalton large T antigen in both permissive and nonpermissive cells. This large T antigen functioned in the initiation of viral DNA replication and in the transformation of nonpermissive cells. T-antigen synthesis by this transposed genome had the characteristics of late transcription, thus indicating that functional large T antigen of simian virus 40 is not required for the initiation of late transcription.

Secondary structure model for the complete simian virus 50 late precursor mRNA

Structures for all sequences containing less than 1790 nucleotides in the 2600 nucleotide late region of the SV40 virus have been computed and saved on magnetic tape. Previously the longest sequence whose secondary structure was calculated in a single computer run contained 950 nucleotides. In the past, analysis of long molecules required numerous repeated, partially overlapping computations on much shorter segments. The structure obtained for the late half of the SV40 is Y-shaped with two unequal arms. It has 52 short hairpins. Two long range interactions between nucleotides near 650 and 1350 and between 1450 and 2450 appear to play an important role. The first is within the 16S intron; the second is in the 3' exon. The 5' and 3' ends of the molecule are close to each other and are found in the major elongated stem in the vicinity of the fork.

Variation in the polyadenylylation site of bovine prolactin mRNA

The poly(A) site of bovine prolactin (bPRL) mRNA was examined by phased priming of cDNA synthesis with oligodeoxynucleotides of the general sequence d(pT8-N-N'). The existence of multiple poly(A)-adjacent sequences in bPRL mRNA was indicated by the production of specific chain-termination fragments with at least three d(pT8-N-N') sequences. Comparison of the sequence bands produced by initiation of cDNA synthesis on the bPRL mRNA template with d(pT8-A-G), d(pT8-G-A), and d(pT8-C-G) revealed a shifted pattern of identical fragments. The shift in position of related sequence bands on the gel suggested that the difference in length of the three major bPRL mRNA species occurred within a span of 12 nucleotides. Sequence analysis conducted with the three d(pT8-N-N') primers gave identical nucleotide sequences for the 3' noncoding region of the bPRL mRNA species and suggested that the mRNA molecules were heterogeneous in length. The existence of multiple poly(A) sites was confirmed by determination of the nucleotide sequence of bPRL cDNA clones containing two of the major poly(A)-adjacent sequences predicted by the oligodeoxynucleotide primers. The mRNA molecules containing these multiple poly(A)-addition sites were shown to be present in the bPRL mRNA obtained from a single pituitary gland. The variation in the poly(A) junction of bPRL mRNA may be a reflection of the processing events at the 3' terminus of mRNAs.

Synthesis of stable unspliced mRNA from an intronless simian virus 40--rat preproinsulin gene recombinant

We constructed a recombinant DNA molecule carrying the coding region and the 3' flanking sequences of the rat preproinsulin I gene, replacing the late region of a simian virus 40 (SV40) viral vector. The sequences making up the single intron of the preproinsulin I gene, located within the nontranslated leader region, as well as all of the 5' flanking sequences, have been deleted. The sequences remaining within the late transcriptional unit of SV40 do not retain a functional intron. This "intronless" mutant nevertheless directs the synthesis of substantial quantities of unspliced stable hybrid transcripts that are translated into polypeptides with insulin immunoreactivity. Two novel 5' termini, not used in wild-type SV40 transcripts, have been detected in the majority of the hybrid RNA molecules. These are located at analogous positions in both of the late SV40 72-base-pair repeats.

Simian virus 40 early mRNA's contain multiple 5' termini upstream and downstream from a Hogness-Goldberg sequence; a shift in 5' termini during the lytic cycle is mediated by large T antigen

We have used primer-directed synthesis, separation, and sequencing of cDNA's to identify and localize the 5' termini of simian virus 40 early mRNA's. We have examined polyadenylated RNAs obtained from whole cytoplasm and polysomes of two transformed lines and from the cytoplasm of infected cells early and late in the lytic cycle, and we have attempted to correlate the results of our cDNA analyses with recent analyses of early cap structures. We have found that early mRNA's from transformed cells have three principal 5' termini, at residues 5,150, 5,154, and 5,155, with terminal transcribed sequences of CU, GC, and GG, respectively. These termini lie 21 to 26 nucleotides downstream from the early Hogness-Goldberg sequence. Transformed cell early mRNA's also contain a series of less abundant 5' termini that are copied from DNA sequences as far as 80 nucleotides downstream and a minimum of 70 to 75 nucleotides upstream from the Hogness-Goldberg sequence. The templates for the upstream 5' termini and the late simian virus 40 mRNA's overlap by a minimum of 60 to 65 nucleotides. Early mRNA's isolated from cells early in infection contain the same three principal 5' termini and downstream minor 5' termini as transformed cell mRNA's, but they lack 5' termini upstream from the Hogness-Goldberg sequence. With the onset of the late lytic phase, there is a progressive decreases in the utilization of the three principal 5' termini and additional downstream 5' termini and a progressive increase in the utilization of four major termini at residues 5,190 to 5,194, which are 10 to 15 nucleotides upstream from the Hogness-Goldberg sequence. With the onset of the late lytic phase, there is a progressive decrease in the utilization of the three principal 5' termini and additional downstream 5' termini and a progressive increase in the utilization of four major termini at residues 5,190 to 5,194, which are 10 to 15 nucleotides upstream from the Hogness-Goldberg sequence. This shift is evident in cells infected with a tsA mutant at the permissive temperature, but is aborted by growth at or shift-up to a restrictive temperature. Thus, this shift is mediated by the gene A product, large T antigen. We present two models, which are mutually exclusive, to account for the role of T antigen in the early-late shift. One involves transcription late in infection on a new DNA template synthesized during DNA replication. The second involves inhibition of initiation of early transcription at residues 5,150 to 5,155 and other downstream sites and a shift of transcription initiation principally to the upstream sites as a result of the binding of T antigen to two sites on simian virus 40 DNA downstream from the Hogness-Goldberg sequence.

Nuclear RNA is spliced in the absence of poly(A) addition

Splicing of newly formed nuclear RNA transcripts has been demonstrated during adenovirus type 2 (Ad2) mRNA formation in HeLa cells in the presence of "cordycepin," 3' deoxyadenosine, a drug that stops poly(A) addition to nuclear RNA. Nuclear RNA prepared from Ad2-infected cells after a 30 min label time in the presence or absence of 3' deoxyadenosine was hybridized to and eluted from Ad2 DNA sequences in the transcription units of region E1b and region E2. The nuclear RNA from the 3' dA-treated cells did not contain poly(A) but did contain Ad2-specific molecules approximately 200 to 250 bases shorter than the spliced mRNAs of the control infected cells. In addition, the approximately 2 kb RNA from Ad2 region E2 was shown to have sequences that lie more than 3.5 kb apart on the DNA, suggesting that correct cutting and splicing of the primary transcript in the absence of poly(A) synthesis had occurred. Therefore, although poly(A) addition usually precedes splicing during mRNA formation, poly(A) is not required for splicing.

Expression of the mouse dihydrofolate reductase complementary deoxyribonucleic acid in simian virus 40 vectors

A mouse complementary deoxyribonucleic acid segment coding for the enzyme dihydrofolate reductase has been cloned in two general classes of vectors containing simian virus 40 deoxyribonucleic acid: (i) those that can be propagated as virions in permissive cells and (ii) those that can be introduced into and maintained stably in various mammalian cells. Both types of vectors express the mouse dihydrofolate reductase by using signals supplied by simian virus 40 deoxyribonucleic acid sequences. Moreover, plasmid vectors carrying the complementary deoxyribonucleic acid segment can complement Chinese hamster ovary cells lacking dihydrofolate reductase.

Transformation of rat cells by an altered polyoma virus genome expressing only the middle-T protein

A modified polyoma virus genome has been constructed which can encode the middle-T protein, but not the large-T or small-T proteins. This was achieved, starting with the full length viral DNA inserted into a plasmid vector, by replacing a small genomic restriction fragment spanning the middle-T intervening sequence with the equivalent fragment from a cloned partial cDNA copy of the middle-T protein mRNA. Transfection of the modified viral DNA into cultured rat cells efficiently induced the formation of transformed cell foci which gave rise to cell lines that grew as tumours after injection into Fisher rats. The only viral early-region antigen synthesized by the cell lines was the middle-T protein. Expression of the middle-t protein is therefore sufficient to establish and maintain a transformed state. The viral mRNA produced by two of the transformed cell lines was structurally indistinguishable from the normal middle-T mRNA found in productively infected cells, suggesting that RNA splicing is not an essential step in the biogenesis of this messenger.

tRNA punctuation model of RNA processing in human mitochondria

A 3'-end proximal segment of most of the putative mRNAs encoded in the heavy strand of HeLa cell mtDNA has been partially sequences and aligned with the DNA sequence. In all cases, the 3'-end nucleotide of the individual mRNA coding sequences has been found to be immediately contiguous to a tRNA gene or another mRNA coding sequence. These and previous results indicate that the heavy (H) strand sequences coding for the rRNA, poly(A)-containing RNA and tRNA species form a continuum extending over almost the entire length of this strand. We propose that the H strand is transcribed into a single polycistronic RNA molecule, which is processed later into mature species by precise endonucleolytic cleavages which occur, in most cases, immediately before and after a tRNA sequence.

Unspliced functional late 19S mRNAs containing intervening sequences are produced by a late leader mutant of simian virus 40

dl-805 is a viable deletion mutant of simian virus 40 lacking 187 of the 202 nucleotides coding for the principal leader of the wild-type viral late mRNAs. The structures of the mutant late 16S and 19S RNAs and proteins were examined with the following principal findings. (i) The vast majority, if not all, of the 19S RNAs are unspliced over their entire length. These RNAs contain intervening sequences and serve as mRNAs. The vast majority, if not all, of the 16S RNAs, however, retain the characteristic wild-type splice. (ii) Mutant 16S and 19S RNAs do not terminate at residue 243 (located six nucleotides upstream from the 5' end of the deleted DNA segment), the principal 5' terminus of the wild-type late mRNAs; rather, they begin at a series of sites, mostly upstream, used infrequently or not at all by wild-type virus. (iii) Despite the presence of altered late mRNAs, dl-805 late proteins have electrophoretic mobilities similar to those of wild-type late proteins, and mutant virions contain the same relative quantities of late proteins as wild-type virions.

The relationship between the SV40 genome and viral mRNA

Studies of SV40 DNA and mRNA sequences have revealed a surprising complexity in the biogenesis of SV40 RNA. SV40 late mRNA shows heterogeneity in 5' ends, as well as internal splicing patterns. There may be coupling between different splices within the mRNA precursors and splicing is not strictly sequential. Translation may initiate at the second or third downstream AUG triplet, rather than at the first initiation codon of the mRNA. The possibility exists that translation may initiate on the same mRNA at more than one initiation codon. The DNA in proximity to the major 5' ends of late mRNA is not essential for transcription. Deletion mutants removing DNA encoding the segments of the leader sequence of late SV40 mRNA show effects on preferred transcription initiation sites both upstream and downstream. This suggests that relatively long stretches of DNA may play a role in determining the sites of transcription initiation.

Simian virus 40 early mRNA's in lytically infected and transformed cells contain six 5'-terminal caps

Late simian virus 40 (SV40) mRNA contains eight different cap structures which we have previously identified and mapped on the viral genome. As reported here, 5'-cap heterogeneity is a common feature to both the early and the late SV40 mRNA's. methyl-3H-labeled viral mRNA was purified from cells infected at 41 degrees C with SV40 mutant tsA209. Three different cap cores were identified: m7GpppGm, m7GpppCm, and m7GpppAm. An average of three to four m6A residues per mRNA molecule was found. RNase T2-resistant 32P-labeled early caps from tsA209-infected cells isolated and characterized. Six distinct cap I structures were identified: m7GpppCmpU (30%), m7GpppGmpC (24%), m7GpppAmpG (18%), m7GpppGmpU (13%), m7GpppGmpG (12%), and m7GpppAmpU (3%). A similar 5'-end heterogeneity was observed in early SV40 mRNA from BSC-1 cells infected with wild-type SV40 strain 777 in the presence of cytosine arabinoside and in the SV40 UV-transformed permissive line C-6. Five of these capped dinucleotides are complementary to DNA sequences at 0.66 map unit in a region previously identified by the primer extension method (Reddy et al., J. Virol. 30:279-296, 1979; Thompson et al., J. Virol. 31:437-438, 1979) as the 5' end of the early message. DNA sequences upstream from this region contain the TATTTAT (Hogness-Goldberg box), which is missing from upstream of the 5'-cap sites of late SV40 mRNA. Thus, 5'-end heterogeneity is not necessarily related to the presence or the absence of this putative transcriptional "initiation signal." When the possibility that SV40 5' caps represent transcriptional initiation sites is considered, the data also suggest that, on SV40 DNA, eucaryotic RNA polymerase II initiates transcription at multiple nucleotide sequences, including pyrimidines.

Nucleotide sequence at polyoma VP1 mRNA splice sites

Double-stranded DNA complementary to total cytoplasmic polyadenylated RNA isolated late in infection from polyoma virus-infected mouse 3T6 cells was cloned in Escherichia coli by using the large HindIII-BamHI fragment of pBR322 plasmid DNA. Polyoma-specific DNA inserts were detected by hybridization, and then nucleotide sequences were determined from two clones. The sequence of the (formula see text) with prototypical mammalian splice sites, and the dashed arrows indicate possible alternative splice sites leading to the same spliced product. A sequence of 897 nucleotides was spliced out of the primary transcript during the processing of the mature VP1 mRNA. Restriction enzyme mapping with four other independently isolated clones indicates that these are the major splicing signals for the VP1 message. The distal splice site is 48 nucleotides upstream from the initiator codon.

Simian virus 40 transcriptional complexes incorporate mercurated nucleotides into RNA in vitro

Simian virus 40 Sarkosyl transcriptional complexes incorporated mercurated nucleotide precursors into preinitiated RNA chains. Synthesis with mercurated precursors was three- to fivefold slower than with nonmercurated nucleotides (12 to 20 pmol per 10(6) cells per h at 25 degrees C), and 50 to 70% of the RNA product bound specifically to sulfhydryl-agarose. The amount of mercurated CMP incorporated into RNA was measured by specific binding of [35S]cysteine to the mercury residues. More than 90% of the mercurated RNA hybridized to simian virus 40 DNA.

The Role of the poly(A) sequence in mammalian messenger RNA

The poly(A) sequence is added to 3' termini of nuclear RNA segments destined to become part of the mRNA, and may play an essential role in the selection of these segments. It appears to be required for at least some of the splicing events involved in mRNA processing. In the cytoplasm, the poly(A) segment is the target of a degradation process which causes its gradual shortening, and leads to a heterogeneous steady-state poly(A)-size distribution. Complete loss of the poly(A) is probably followed by inactivation of the mRNA, since chains depleted of poly(A) do not accumulate in the cells. A role for this sequence in the promotion of mRNA stability is suggested by the behavior of globin mRNA depleted of poly(A) after injection into frog oocytes. The poly(A) shortening process may be part of the mRNA inactivation mechanism, as indicated by the greater sensitivity to degradation of the poly(A) of some short-lived mRNAs. However, the stochastic mRNA decay implies that new and old mRNA chains, with long and short poly(A) segments, respectively are equally susceptible to inactivation. The poly(A)-lacking histone mRNAs are stable only in cells engaged in DNA replication. Present knowledge favors a role for poly(A) in the control of mRNA stability. Loss of this sequence could be controlled through modulation of poly(A)-protein interactions or through masking of a sequence directly adjacent to the poly(A). In the nucleus, the poly(A) sequence could also serve as stabilizing agent, but, in addition, it might interact with the splicing machinery.

General occurrence and transcription of intervening sequences in mouse genes expressed via polyadenylated mRNA

cDNA of modal size approximately 1600 nucleotides, transcribed from mouse brain polyadenylated mRNA, was annealed with excess of high molecular weight (approximately kb) genomic DNA. The S1 nuclease method was then applied to determine possible sequence discontinuity between the cDNA and genomic DNA. A substantial reduction in the average size of the annealed cDNA was observed following S1 nuclease treatment. Large single copy genomic DNA, annealed with excess high molecular weight DNA, and cDNA, hybridized with its template mRNA, were resistant to cleavage by S1 nuclease. We interpret these results to indicate a high frequency of discontinuous coding sequences in the genomic DNA that annealed with the cDNA. The same result was obtained using fractionated cDNA, enriched in transcripts of relatively infrequent or abundant mRNA species. The result obtained with the infrequent sequence class cDNA indicates that tens of thousands of split genes exist in the mouse genome. Extensive cleavage of the cDNA by S1 nuclease was also observed after hybridization with greater than 30S nuclear RNA, indicating that intervening sequences are generally transcribed.

Transcripts from the adenovirus-2 major late promoter yield a single early family of 3' coterminal mRNAs and five late families

The major late promoter of adeovirus-2 is located at coordinate 16.45 and initiates synthesis of nuclear precursors that are processed into mRNAs which fall into five 3- co-terminal families, L1-L5. These mRNAs all share a common tripartite 5' leader with a capped terminus encoded at th RNA initiation site. We show that the coorindate 16.45 RNA initiation site is also an early promoter, and yields transcripts detectable as early as 1 hr post-infection, prior to DNA replication and the early-late switch at 6-8 hr. Polyadenylated cytoplasmic RNA from the first 3- co-terminal family, L1, is also produced from the earliest stages of infection. L1 mRNA accumulates in the cytoplasm in the presence of cycloheximide, which blocks DNA replication and the onset of the late phase. Early nuclear RNA contains the same capped 5' terminal RNAase T-1 undecanucleotide and promoter proximal oligonucleotides present in late transcripts. This implies that precisely the same transcription start site is utilized for early L1 mRNA synthesis as is used during the late stage for L1-L5 late mRNA synthesis. In contrast to the early apperance of L1 mRNA, neither L2 nor L3 mRNAs are detected until 5-6 hr post infection. We cnclude that a major event in the Ad-2 early-late switch is a novel form of control which activates L2-L5 mRNA production.

Simian virus 40-associated small RNA: mapping on the simian virus 40 genome and characterization of its synthesis

The simian virus 40 (SV40)-associated small RNA (SAS-RNA) has previously been shown to arise late in SV40 lytic infection and to bear homology with the SV40 early mRNA's, or the SV40 genome, at map position 0.21. By using hybridization analysis, we determined that the SAS-RNA is between 62 and 65 nucleotides in length and its homology region lies between nucleotides 2760 and 2825 of the SV40 late(+) DNA strand. Viable deletion mutants which lacked part or all of this region made no SAS-RNA, strongly indicating that this is the coding region of the SAS-RNA. The expected sequence for the SAS-RNA, determined from the DNA sequence between nucleotides 2760 and 2825, appeared to be very pyrimidine rich (76% uridine and cytidine). Deletion or alteration of sequences immediately preceding the SAS-RNA coding region (approximately nucleotides 2716 to 2748) resulted in the loss of SAS-RNA production. These sequences may be part of a promotor for SAS-RNA synthesis or a processing site for its excision from long nuclear late transcripts. Under growth conditions where late transcription was not fully initiated (tsA58 at 41 degrees C; wild-type SV40 in the presence of 1-beta-D-arabinofuranosylcytosine), no SAS-RNA was produced, indicating that the expression of the SAS-RNA is regulated by a mechanism related to the control of late transcription.

Characterisation of polyoma late mRNA leader sequences by molecular cloning and DNA sequence analysis

The leader sequences of two of the three polyoma virus late mRNAs were characterised by molecular cloning and DNA sequence analysis. A short single-stranded DNA fragment complementary to the 5' end of the body of mVP1 was used to prime cDNA synthesis, and double-stranded cDNA was inserted into a derivative of pAT 153. Analysis of fourteen mVP1 cDNAs and two mVP3 cDNAs allowed the precise determination of the leader-body joints, and demonstrated that the majority of polyoma late leader sequences consist of exact tandem repeats of a 57 nucleotide sequence present only once in the genomic DNA at 66-67 m.u. The sequences in the genomic DNA borderline this unit are typical of those found at RNA splice points. Leader sequences contained on average three to four repeat units. Nuclease S1 mapping of total late mRNA demonstrated that most mRNA 5' ends map heterogeneously in the 50 nucleotides 5' to the repeated sequence unit. The structures of the leader sequences strongly suggest that they are generated by appropriate splicing events from a tandemly repeated transcript of the entire circular viral genome.