Splicing of the adenovirus-2 E1A 13S mRNA requires a minimal intron length and specific intron signals.

The adenovirus E1A region encodes three overlapping mRNAs, designated 9S, 12S and 13S. They differ from each other with regard to the length of the intron which is removed by RNA splicing. We have constructed E1A genes with deletions and insertions in the intervening sequence that is common to all three E1A mRNAs, in a search for signals which influence splicing of the 13S mRNA. Mutant plasmids were transfected into HeLa cells and the transiently expressed E1A mRNAs characterized by the S1 protection assay. The results show that five upstream and 20 downstream nucleotides are sufficient to allow for a correct utilization of the 5'-splice junction for the E1A 13S mRNA. Moreover, we show that a minimal intron length of 78 nucleotides is required for efficient 13S mRNA splicing. The ability of mutants with large intron deletions to maturate a 13S mRNA could partially be restored by expanding the intron length with phage lambda sequences. However, in no case was the normal splicing efficiency obtained with these mutants. In contrast, one mutant in which sequences from the authentic 13S mRNA intron were used to expand the intron expressed almost normal levels of 13S mRNA, thus suggesting that signals which specifically promote 13S mRNA splicing exist.     

A U1 small nuclear ribonucleoprotein particle with altered specificity induces alternative splicing of an adenovirus E1A mRNA precursor.

We have altered the specificity of U1 small nuclear RNA by replacing its 5' splice site recognition sequence (nucleotides 3 to 11) with sequences complementary to other regions of either the adenovirus E1A or the rabbit beta-globin mRNA precursor. We then used a HeLa cell transient expression assay to test whether such altered U1 small nuclear ribonucleoprotein particles (snRNPs) could interfere with splicing of the targeted mRNA precursors. The altered U1 snRNPs were able to cause novel splicing of the E1A mRNA precursor, minor changes in the ratio of E1A 12 to 13S mRNAs, and modest nuclear accumulation of beta-globin mRNA precursors with either one of the two introns removed. Most of the altered U1 snRNPs did not affect the level of mature cytoplasmic mRNA significantly, but in one case an altered U1 snRNP (alpha 1) whose intended target was located downstream from the adenovirus E1A 12S 5' splice site was able to reduce the level of cytoplasmic 12S mRNA by approximately 60% and that of 13S mRNA by 90%. This alpha 1 snRNP induced an additional E1A splice, resulting in the appearance of 10 and 11S E1A mRNAs normally found only late in adenovirus infection. Thus, a trans-acting factor can induce alternative splicing. Surprisingly, the effects of alpha 1 on E1A splicing were not abolished by deleting the intended target sequence on the mRNA precursor.     

Differential splicing yields novel adenovirus 5 E1A mRNAs that encode 30 kd and 35 kd proteins.

In addition to the protein products of the adenovirus E1A 13S and 12S mRNAs, monoclonal antibodies specific for the E1A proteins immunoprecipitate polypeptides with relative mol. wt of 30,000 (30 kd) and 35,000 (35 kd) from extracts of infected cells. The 30 kd and 35 kd proteins are encoded by novel mRNAs referred to as the 10S and 11S mRNAs, respectively. These two mRNAs arise from differential splicing of the E1A precursor RNA. For the 10S mRNA, the precursor is spliced twice, once removing the region between nucleotides 637 and 854 and once between 974 and 1229. The splice between nucleotides 974 and 1229 is identical to the one used for the processing of the 12S mRNA. Synthesis of the 11S mRNA also utilizes two splicing events. One of these is identical to the 637/854 splice of the 10S mRNA, and the other removes the region between nucleotides 1112 and 1229, a splice junction also found in the 13S mRNA. All four mRNAs used the same reading frame and, therefore, code for related proteins. The products of the 10S and 11S mRNAs are identical to the products of the 12S and 13S mRNAs, respectively, except for an internal stretch of 27 amino acids removed by the 637/854 splice. Within this segment is a group of amino acid residues that is highly conserved between different adenovirus serotypes. Mutant adenoviruses in which the wild-type E1A sequences have been replaced with cDNA copies of the 10S or 11S mRNAs are defective for growth on HeLa cells suggesting that this region is important for viral growth.(ABSTRACT TRUNCATED AT 250 WORDS)     

Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA.

The rat erbA alpha locus encodes two overlapping mRNAs, alpha 1 and alpha 2, which are identical except for their most 3' exons. alpha 1 mRNA encodes a thyroid hormone receptor, while alpha 2 encodes an altered ligand binding domain of unknown function. Previous studies have shown that the ratio of alpha 1 to alpha 2 is highest in cells expressing a high level of a third RNA, Rev-ErbA alpha mRNA, which is transcribed in the opposite direction and is complementary to alpha 2 but not alpha 1 mRNA. It was hypothesized that base pairing with Rev-ErbA alpha blocks splicing of alpha 2 mRNA, thereby favoring formation of the non-overlapping alpha 1. To test this model, a system was developed in which alpha 2 pre-mRNAs were accurately spliced in vitro. Splicing was inhibited by the addition of a 5-fold excess of antisense RNAs containing the 3' end of Rev-ErbA alpha mRNA. Both an antisense RNA extending across the 3' splice site and a shorter RNA complementary only to exon sequences efficiently blocked splicing. However, splicing was only inhibited by complementary RNAs. These observations are consistent with a mechanism in which base pairing with a complementary RNA regulates alternative processing of alpha 1 and alpha 2 mRNAs.     

Splicing of cauliflower mosaic virus 35S RNA is essential for viral infectivity.

A splicing event essential for the infectivity of a plant pararetrovirus has been characterized. Transient expression experiments using reporter constructs revealed a splice donor site in the leader sequence of the cauliflower mosaic virus (CaMV) 35S RNA and three additional splice donor sites within open reading frame (ORF) I. All four donors use the same splice acceptor within ORF II. Splicing between the leader and ORF II produces an mRNA from which ORF III and, in the presence of the CaMV translational transactivator, ORF IV can be translated efficiently. The other three splicing events produce RNAs encoding ORF I-II in-frame fusions. All four spliced CaMV RNAs were detected in CaMV-infected plants. Virus mutants in which the splice acceptor site in ORF II is inactivated are not infectious, indicating that splicing plays an essential role in the CaMV life cycle. The results presented here suggest a model for viral gene expression in which RNA splicing is required to provide appropriate substrate mRNAs for the specialized translation mechanisms of CaMV.     

Regulation of the appearance of cytoplasmic RNAs from region 1 of the adenovirus 2 genome

The time-course of appearance of cytoplasmic RNA species coded by the region 9 to 10.7 on the adenovirus 2 genome (early region 1) has been examined using specific DNA probes. Hybridization with restriction endonuclease fragments of viral DNA resolved five cytoplasmic RNAs. A 22 S RNA contains sequences to the right of map position 4.4. One 13 S RNA (13 S_L) maps to the left of this site, while an RNA of similar size (13 S_f) is transcribed from two separate regions to the right of 4.4. Each 13 S RNA shares 3′ sequences with a distinct 9 S RNA. Sequences in 13S_f RNA are also present in the 22 S species. These mapping studies have allowed the identification of probes that can be used to assay each RNA after fractionation by size.During productive infection, each RNA species has a characteristic rate of appearance in the cytoplasm; 22 S and 13 S_L RNA accumulate at a constant rate throughout infection. Initially 13 S_f RNA appears at a rate substantially lower than the 22 S and 13 S_L, RNAs. At late times accumulation of 13 S_f RNA is stimulated more than 50-fold, until its appearance exceeds that of the other “early” RNAs. The 9 S RNAs are detected only after viral DNA replication begins. The rate of labeling of each approaches that of its colinear 13 S RNA. The results demonstrate a complex regulatory pattern for region 1 RNAs. Regulatory events must account for: (1) continued synthesis of early RNAs at late times; (2) increased accumulation of 13 S_f RNA; (3) the turn on of 9 S synthesis; and (4) balanced rates of appearance of the colinear 13 S and 9 S RNAs at late times.     

Immortalization of rat embryo fibroblasts by an adenovirus 2 mutant expressing a single functional E1a protein.

Expression of the adenovirus E1a and E1b genes is required for transformation of nonpermissive rodent cells. Differential splicing of the E1a precursor RNA molecules results in the production of two early mRNAs, 13S and 12S, which encode a 289-amino-acid-residue (289R) and 243R protein, respectively. Previously we constructed a mutant virus, dl231, which can only produce normal 289R protein from the E1a gene. In this report we demonstrate that dl231 induced focal transformation of primary rat embryo fibroblasts at 20% of the level of wild-type virus. dl231 transformants were immortalized and produced normal levels of E1a 13S and E1b mRNAs but only minute levels of defective E1a 12S mRNA. These transformants only minimally expressed the transformation phenotype and were similar to untransformed cells. Unlike wild-type transformants, they had a more fibroblastic morphology, were contact inhibited, grew to only low saturation density, and were limited in their ability to grow in an anchorage-independent manner in soft agar. We conclude that the 289R E1a protein can mediate immortalization of primary cells and that the 243R E1a protein is required to elicit the full transformation phenotype.     

U1, U2, and U4/U6 small nuclear ribonucleoproteins are required for in vitro splicing but not polyadenylation

The requirement for individual U RNAs in splicing and polyadenylation was investigated using oligonucleotide-directed cleavage of snRNAs in in vitro processing extracts. Cleavage of U1, U2, or U4 RNA inhibited splicing but not polyadenylation of short precursor RNAs. Thus each snRNA and the snRNP in which it is assembled participates in the splicing reaction. Splicing activity was recovered when extracts containing cleaved U RNAs were mixed in pairwise combinations, indicating that U1, U2, and U4/U6 snRNPs independently interact with the assembling spliceosome. The involvement of multiple snRNPs in the splicing of simple precursor RNAs suggests that the spliceosome is a large complex assembly consisting of multiple snRNPs whose activity is dependent on the structural integrity of the individual U RNAs.     

Cell-free translation of adenovirus 2 E1a- and E1b-specific mRNAs and evidence that E1a-related polypeptides are produced from E1a-E1b overlapping mRNA

We have characterized the polypeptides translated in vitro by mRNAs of early region 1 (E1) of human adenovirus (Ad) type 2. Poly (A+) polyribosomal RNA was isolated from early Ad2-infected cells, the viral specific mRNAs were selected by hybridization to Ad2 E1a and E1b DNA, and the mRNAs were translated in vitro using [35S]methionine as a labeled precursor with a rabbit reticulocyte lysate. E1a-selected mRNA was translated to the 45-58-kDa cluster of polypeptides. We show here that E1b-selected mRNA can also be translated to the 45-58-kDa cluster of polypeptides in addition to the major 19-kDa polypeptide. The E1b 58-kDa polypeptide was produced only at a low level unless E1b mRNA is fractionated before translation to enrich for the 58-kDa mRNA. Translation of E1b region-selected mRNAs that have been fractionated by size shows that the 22 S mRNA fraction is translated to at least the 53-58-kDa E1a-related polypeptides as well as to E1b 58- and 19-kDa polypeptides. Our experiments suggest that the 22 S mRNA fraction includes E1a-E1b overlapping mRNA which was translated to E1a-related polypeptides as well as E1b 22 S mRNA. When compared by two-dimensional gel electrophoresis and by tryptic peptide mapping, the cluster of polypeptides translated from E1a-selected mRNA and the cluster translated from E1b-selected mRNA were distinguishable. A possible explanation for this is discussed, based upon splicing sites of the E1a-E1b overlapping mRNA which would result in an amino acid sequence with a COOH-terminal end slightly different from that of E1a polypeptides.     

Polypyrimidine tract-binding protein 2 binds to selective, intronic messenger RNA and microRNA targets in the mouse testis

Here we use an in vivo cross-linking and immunoprecipitation procedure to detect RNA targets of the multifunctional RNA-binding protein polypyrimidine tract-binding protein (PTBP) 2 in mouse testis. Eleven known mRNAs, including Ptbp2 mRNA, 28 RNAs matching intron sequences, and 12 small RNAs and repeat sequences are identified. The specificity of interaction between PTBP2 and its target RNAs was confirmed using RNA interference with mouse N2A cells. Reduction of PTBP2 levels led to decreases in 7 of 10 of the mRNAs, to the repression of alternative splicing of introns, and to reductions in specific miRNAs.     

Integration and transcription of group C human adenovirus sequences in the DNA of five lines of transformed rat cells

We have used the Southern blotting technique to analyze the integration patterns of human adenovirus sequences in the DNA of four rat cell lines, F17, 8617, T2C4 and F4, which were transformed by Ad-2 virus, and 5RK clone 6, which was transformed by Ad-5 HindIII-G fragment. We have also analyzed the Ad-specific messenger RNAs synthesized in these cell lines, in 293 cells (an Ad-5 transformed human cell line), and in Ad-2 early infected human KB cells, using the RNA geltransfer hybridization technique. We were interested in whether the Ad sequences are integrated, what the integration patterns are, whether the transforming region is present in an intact form, and whether the transforming region and other early regions are expressed at the mRNA level.Our results show that the integration patterns of Ad sequences range from simple to quite complex. Cells from line 8617 contain a single copy of right-end sequences flanked by left-end sequences. T2C4 cells have four different left-end sequences and two different right-end sequences. 5RK cells contain multiple different pieces of left-end sequences. In agreement with the results of Sambrook et al. (1979a,b), F17 cells contain a single copy of the left 17% of the genome, and F4 cells contain multiple copies of the right 5% of the genome fused to the left ~ 68% of the genome. The complete Ad genome is not present in any of the cell lines, and different regions may not be equimolar. There are no specific sites on the cellular or viral genome at which integration occurs. In 8617, F17 and F4 cells the Ad-2 sequences appear to be located close together on a single chromosome, suggesting that the Ad sequences in these cells arose from a single integration event. F17, 8617, T2C4, F4, and probably 5RK, cells all have an intact early region E1a (map position 1·3–4·6); F17, 8617, T2C4 and F4 cells also have E1b (m.p. 4·6–11·2) intact. E1a and E1b are the regions responsible for transformation. 8617 cells also have an intact early region E4 (m.p. 99-91·5) and T2C4 cells have an intact early region E3 (m.p. 76–86).Ad-2 early infected KB cells were shown to synthesize major E1a-specific mRNAs of 13 S, 12 S and 9 S, and major E1b-specific mRNAs of 22 S and 13 S. All the transformed cells synthesize the E1a 13 S and E1a 12 S mRNAs, and all cells except 5RK synthesize the E1b 22 S and E1b 13 S mRNAs. Early infected KB cells synthesize E3-specific mRNAs of 26 S, 24 S, 22 S, 19 S, 12 S and 9 S: T2C4 cells synthesize the major 22 S and 19 S RNA species, and possibly the less pronounced E3 mRNAs. Early infected cells and 8617 cells synthesize E4-specific mRNAs of 19 S, 17 S, 14 S, 12 S, 11 S, 9 S and 8 S. 8617 cells also synthesize E4 mRNAs of about 23 to 24 S and 21 S. F4 cells synthesize 24 S and 19 S hybrid mRNAs that contain both E4 and E1a sequences: these RNAs arise because F4 cells contain a portion of the E4 region fused to the left end (m.p. 0) of the genome.Our results, as well as those from other laboratories, are consistent with the idea that the transformed phenotype of Ad transformed cells is maintained by expression of Ad genes in E1a and E1b.