A protein factor, ASF, controls cell-specific alternative splicing of SV40 early pre-mRNA in vitro

SV40 early pre-mRNA is alternatively spliced by utilization of two different 5' splice sites and a shared 3' splice site to produce large T and small t mRNAs. The ratio of small t to large T mRNAs produced in human embryonic kidney 293 cells is 10- to 20-fold greater than in other mammalian cells, suggesting the existence of a 293 cell-specific factor that modulates alternative splicing. Here we show that nuclear extracts from 293 cells give rise to significantly more small t splicing than do extracts from HeLa cells. Using an in vitro complementation assay, we have characterized and extensively purified a factor from 293 extracts that brings about striking increases in small t splicing with concomitant decreases in large T splicing. The factor is heat sensitive and micrococcal nuclease resistant, suggesting that it is a protein lacking an accessible RNA component. Purification of the alternative splicing factor indicates that the activity is contained in one of several possibly related polypeptides of 30-35 kd.

Polyoma virus small tumor antigen pre-mRNA splicing requires cooperation between two 3' splice sites

We have studied splicing of the polyoma virus early region pre-mRNA in vitro. This RNA is alternatively spliced in vivo to produce mRNA encoding the large, middle-sized (MTAg), and small (StAg) tumor antigens. Our primary interest was to learn how the 48-nucleotide StAg intron is excised, because the length of this intron is significantly less than the apparent minimum established for mammalian introns. Although the products of all three splices are detected in vitro, characterization of the pathway and sequence requirements of StAg splicing suggests that splicing factors interact with the precursor RNA in an unexpected way to catalyze removal of this intron. Specifically, StAg splicing uses either of two lariat branch points, one of which is located only 4 nucleotides from the 3' splice site. Furthermore, the StAg splice absolutely requires that the alternative MTAg 3' splice site, located 14 nucleotides downstream of the StAg 3' splice site, be intact. Insertion mutations that increase or decrease the quality of the MTAg pyrimidine stretch enhance or repress StAg as well as MTAg splicing, and a single-base change in the MTAg AG splice acceptor totally blocks both splices. These results demonstrate the ability of two 3' splice sites to cooperate with each other to bring about removal of a single intron.

Oligonucleotide-targeted degradation of U1 and U2 snRNAs reveals differential interactions of simian virus 40 pre-mRNAs with snRNPs

We have investigated the roles of U1 and U2 snRNP particles in SV40 pre-mRNA splicing by oligonucleotide-targeted degradation of U1 or U2 snRNAs in Xenopus laevis oocytes. Microinjection of oligonucleotides complementary to regions of U1 or U2 RNAs either in the presence or absence of SV40 DNA resulted in specific cleavage of the corresponding snRNA. Unexpectedly, degradation of U1 or U2 snRNA was far more extensive when the oligonucleotide was injected without, or prior to, introduction of viral DNA. In either co-injected or pre-injected oocytes, these oligonucleotides caused a dramatic reduction in the accumulation of spliced SV40 mRNA expressed from the viral late region, and a commensurate increase in unspliced late RNA. When pre-injected, two different U2 specific oligonucleotides also inhibited the formation of both large and small tumor antigen spliced early mRNAs. However, even when, by pre-injection of a U1 5' end-specific oligonucleotide, greater than 95% degradation of the U1 snRNA 5' ends occurred in oocytes, no reduction in early pre-mRNA splicing was observed. In contrast, the same U1 5' end oligonucleotide, when added to HeLa splicing extracts, substantially inhibited the splicing of SV40 early pre-mRNA, indicating that U1 mRNP is not totally dispensable for early splicing. These findings confirm and extend our earlier observations which suggested that different pre-mRNAs vary in their requirements for snRNPs.

Factor interactions with the simian virus 40 early pre-mRNA influence branch site selection and alternative splicing

To study the interaction of splicing factors with the simian virus 40 early-region pre-RNA, which can be alternatively spliced to produce large T and small t mRNAs, we used an in vitro RNase protection assay that defines the 5' boundaries of factor-RNA interactions. Protection products reflecting factor interactions with the large T and small t 5' splice sites and with the multiple lariat branch site region were characterized. All protection products were detected very early in the splicing reaction, before the appearance of spliced RNAs. However, protection of the large T 5' splice site was detected well before small t 5' splice site and branch site protection products, which appeared simultaneously. Oligonucleotide-targeted degradation of small nuclear RNAs (snRNAs) revealed that protection of the branch site region, which occurred at multiple sites, required intact U2 snRNA and was enhanced by U1 snRNA, while protection of the large T and small t 5' splice sites required both U1 and U2 snRNAs. Analysis of several pre-RNAs containing mutations in the branch site region suggests that factor interactions involving the multiple copies of the branch site consensus determine the selection of branch points, which is an important factor in the selection of alternative splicing pathways.

The role of the polypyrimidine stretch at the SV40 early pre-mRNA 3′ splice site in alternative splicing

We have studied the role in pre-mRNA splicing of the nucleotide sequence preceding the SV40 early region 3' splice site. Somewhat surprisingly, neither the pyrimidine at the highly conserved -3 position, nor the polypyrimidine stretch that extends from -5 to -15, relative to the 3' splice site, were found to be required for efficient splicing. Mutations that delete this region or create polypurine insertions at position -2 had no significant effects on the efficiency of SV40 early pre-mRNA splicing in vivo or in vitro. Interestingly, however, the pyrimidine content of this region had substantial effects on the alternative splicing pattern of this pre-mRNA in vivo. Mutations that increased the number of pyrimidine residues resulted in more efficient utilization of the large T antigen mRNA 5' splice site relative to the small t 5' splice site, while mutations that increased the purine content enhanced small t mRNA splicing. A possible molecular mechanism for these findings, as well as a model that proposes a role for the polypyrimidine stretch in alternative splicing, are discussed.

Analysis for total sulfite in foods by using rapid distillation followed by redox titration

A rapid and accurate analysis for total sulfite as sulfur dioxide has been developed for foods and food products. The method, which combines a selective distillation cleanup procedure with the selective redox titration of sulfite ion by iodine, has been applied to a variety of foods and food products over a period of time with no significant interference encountered in any matrixes other than garlic and leeks. For the foods analyzed, the method typically shows a detection limit of 10 ppm, a relative standard deviation of 7.5% (compared with 10.4% for similar matrixes by the Monier-Williams method), and recoveries of 97.9 +/- 6.4%. Comparison of results for this method with those obtained using the Monier-Williams method showed a mean value for the distillation/titration method of 241 ppm compared with 242 ppm for the Monier-Williams method. A correlation of 0.991 and odds of a difference between methods of 10.7% (Student's paired t-test (1-alpha) X 100) were obtained for those matrixes where no interferences were encountered with either method.

On-line generation of cyanogen chloride in semiautomated determination of niacin and niacinamide in food products

The current AOAC procedure for semiautomated determination of niacin specifies the use of externally generated cyanogen bromide. Because of the safety concerns in handling this material, we investigated the use of an alternative system of generating cyanogen chloride in situ, using chloramine-T and potassium cyanide. Recovery studies conducted on 9 different food products yielded average recoveries of 101%. A repeatability study resulted in a measured coefficient of variation of 2.9%. The AOAC niacin method was compared with this semiautomated method; 115 paired analyses on 8 different food types over 6 separate analytical replications indicated no significant difference by a paired t-test at the 95% confidence level.

Semiautomated Fluorometric Method for Determination of Vitamin C in Foods: Collaborative Study

Continuous flow automation of the microfluorometric procedure compares favorably with the manual method in sensitivity, specificity, and generality, and reduces the cost of routine vitamin C assay. Fifteen samples of 12 different products of ready-to-eat cereals, fruit juices, and infant formula were sent to 6 collaborators; one sample in each category was sent as blind duplicates. The within-laboratory standard deviations for 5 collaborators on the 3 sets of blind duplicates were 1.23, 0.87, and 3.64 mg/100 g, respectively. Overall, the average relative standard deviation between laboratories was 11.1% (range 4.5-16.6%) for the manual method and 4.99% (range 1.5-12.6%) for the semiautomated method. The method has been adopted official first action.