Synthesis of predominantly unspliced cytoplasmic RNAs by chimeric herpes simplex virus type 1 thymidine kinase-human beta-globin genes

Homology between alpha 2(V) and alpha 1(III) collagen promoters and evidence for negatively acting elements in the alpha 2(V) first intron and 5' flanking sequences

We have isolated a 17 kilobase pair (kb) genomic clone containing the 5' portion of the human alpha 2(V) collagen gene. Nucleotide sequence was determined for 1671 base pairs (bp) comprising the promoter region, first exon and 334 bp of the first intron, and the major transcriptional start site determined by primer extension and S1 nuclease analysis. Sequence comparison revealed the alpha 2(V) promoter to be similar in structure to the promoter of the alpha 1(III) collagen gene. This is the first instance of such similarities between promoter regions of genes encoding different fibrillar collagen chains. Homology, in 5' flanking sequences, extends upstream to about nucleotide -120 in each gene and is particularly striking near the TATTTA sequence (TATA box) present in each promoter. Some homology also surrounds the two transcription start sites. The 5' untranslated regions of the two genes also show strong homology. Chimeric chloramphenicol acetyltransferase (CAT) constructs were prepared with various fragments from the 5' portion of the alpha 2(V) gene. Transient expression assays, in human fibroblasts, localized the functional alpha 2(V) promoter to the region of 5' flanking sequence conserved between the alpha 2(V) and alpha 1(III) genes. Expression assays also identified negatively acting elements, in intron and 5' flanking sequences, which inhibit transcription from the alpha 2(V) promoter.

Authentic Borna disease virus transcripts are spliced less efficiently than cDNA-derived viral RNAs

Borna disease virus (BDV) is a non-segmented, negative-strand RNA virus that replicates and transcribes its genome in the nucleus of infected cells. It uses the cellular splicing machinery to generate a set of alternatively spliced mRNAs from the 2.8 and 7.1 kb primary transcripts, each harbouring two introns. To determine whether splicing of these transcripts is regulated by viral factors, the extent of splicing was studied in infected cells and COS-7 cells transiently transfected with plasmids encoding the 2.8 kb RNA of BDV. Unspliced RNA was found to be the most abundant RNA species in infected cells, whereas viral transcripts lacking both introns were only found in minute amounts. In sharp contrast, plasmid-derived 2.8 kb RNA was predominantly intron 1-spliced and double-spliced. Co-expression of the BDV proteins P, N and X did not influence splicing of plasmid-expressed 2.8 kb RNA. Furthermore, the splicing pattern did not change when the 2.8 kb RNA was expressed in BDV-infected cells. Based on these results we speculate that splicing of authentic BDV transcripts is tightly linked to transcription by the viral polymerase.

Viral RNA export

Viruses can express intron-containing and intronless mRNAs, which are exported by alternative pathways. The study of the nuclear export of these unconventional mRNAs can provide key insights into the normal process of nuclear export and the alternative pathways provide an attractive target for the development of specific antiviral therapies.

Extreme heterogeneity of polyadenylation sites in mRNAs encoding chloroplast RNA-binding proteins in Nicotiana plumbaginifolia

We have previously characterized nuclear cDNA clones encoding two RNA binding proteins, CP-RBP30 and CP-RBP-31, which are targeted to chloroplasts in Nicotiana plumbaginifolia. In this report we describe the analysis of the 3'-untranslated regions (3'-UTRs) in 22 CP-RBP30 and 8 CP-RBP31 clones which reveals that mRNAs encoding both proteins have a very complex polyadenylation pattern. Fourteen distinct poly(A) sites were identified among CP-RBP30 clones and four sites among the CP-RBP31 clones. The authenticity of the sites was confirmed by RNase A/T1 mapping of N. plumbaginifolia RNA. CP-RBP30 provides an extreme example of the heterogeneity known to be a feature of mRNA polyadenylation in higher plants. Using PCR we have demonstrated that CP-RBP genes in N. plumbaginifolia and N. sylvestris, in addition to the previously described introns interrupting the coding region, contain an intron located in the 3' non-coding part of the gene. In the case of the CP-RBP31, we have identified one polyadenylation event occurring in this intron.

Transduction of the human insulin gene via retroviral vectors fails to yield spliced transcripts

Previous reports on retroviral vectors have shown them to be useful for transferring genes into animal cells. Genes placed under the retroviral long terminal repeat (LTR) act as dominant loci in recipient cells and can permanently alter their genotype and phenotype. Previous reports have shown that recombinant retroviruses containing genomic sequences with both introns and exons display a high frequency of deletion and abnormal kinetics of splicing of intron sequences. We report here our findings when a 2.9-kb fragment containing the entire human insulin gene was inserted into a Moloney-derived retroviral vector in the same transcriptional orientation as the LTRs. RNA transcripts synthesized in cells containing such constructs remain unspliced, as assessed by both RNA blot analysis and S1 mapping. Ten subclones derived following viral passage showed no splicing, and failure to splice was observed regardless of cell type or species of origin, or number of viral passages. Thus, genomic sequences containing introns when situated within the context of a retroviral transcript do not in all instances exhibit expected kinetics of splicing.

Conserved quartets near 5' intron junctions in primate nuclear pre-mRNA

Analysis of a 1000 nucleotide span around 664 primate 5' exon/intron junctions revealed frequent recurrences of G-rich runs downstream of the 5' splice sites. In particular, AGGG, GGGA, GGGG, GGGT and TGGG are frequent at this site. Some C-rich quarters are frequent upstream of the 5' splice site. Similar behaviour of these G- and C-rich quartets is indicated for the 587 rodent introns and for a combined eukaryotic file containing 1688 introns. (A)GGG(A) is also frequent in the introns 60 nucleotides upstream of the 3' splice site, and (A)CCC(A) is frequently found in the exons downstream of the 3' site. The same consistent behaviour of the 3' splice sites is obtained as for the 5' sites, for the primates, rodents and combined eukaryotic file. These results suggest that in addition to the well-conserved 5' and 3' splice sequences, exon as well as intron sequences may play a role in nuclear pre-mRNA splicing.

Expression of human uterine tissue-type plasminogen activator in mouse cells using BPV vectors

Human tissue-type plasminogen activator (t-PA) cDNA was cloned from uterine tissue and engineered in expression vectors for production in mouse C127 cells. The vectors consisted of the bovine papilloma virus-1 (BPV-1) genome and t-PA transcriptional unit with a mouse metallothionein (MT-1) promoter at the 5' end and MT-1 genomic sequences or SV40 early introns and polyadenylation signals at the 3' end. Analysis of the expression vectors transfected into cells revealed that t-PA is expressed 100- to 200-fold more with an intronless vector utilizing the SV40 polyadenylation signal than with other, intron-containing vectors. RNA analysis of stable cell lines indicated that t-PA expression levels correlated with mRNA abundance. DNA copy number and transcriptional rate of the MT-1 promoter remained constant in cell lines transformed by different BPV expression vectors. Uterine t-PA produced by recombinant DNA means was enzymatically active and similar in properties to Bowes melanoma t-PA.

A role for exon sequences and splice-site proximity in splice-site selection

Analysis of the in vitro splicing products of RNA precursors containing tandem duplications of the 5' or 3' splice sites of human beta-globin IVS 1 revealed that exon sequences play an important role in the relative use of the duplicated sites. These studies also show that the proximity of the 5' and 3' splice sites is an important determinant in the selection of splice-sites. Deletion, substitution, or even subtle changes of exon sequences can alter the pattern of splice-site selection, and in many cases the splice site adjacent to the altered exon is not used. The relative use of the duplicated splice sites can also be altered by diluting the splicing extract, suggesting that factors involved in splice-site selection are limiting.

Regulation of the expression of the SV40 T-antigen coding gene under the control of an rDNA promoter

We have constructed a hybrid gene in which the SV40 T-antigen coding gene is driven by a mouse rDNA promoter and we have compared its expression to that of an SV40 T-antigen coding gene under the control of its own promoter. The comparison has been carried out in microinjected cells, in transfected cells, and in stable cell lines carrying the respective T-antigen coding genes in an integrated form. These cell lines were derived from ts AF8 cells, a mutant which is temperature sensitive for RNA polymerase II activity. The hybrid gene clearly expresses T-antigen, albeit less efficiently than when the T antigen coding gene is under the control of the SV40-promoter. We also show that the expression of T-antigen by the hybrid gene is 50% inhibited by an antibody against RNA polymerase I. In tsAF8 cells carrying the hybrid gene, T-antigen is still expressed at the restrictive temperature (where RNA polymerase II is inactive) at a level again about 50% of controls. However, our findings also confirm those of Smale and Tjian (Mol. Cell. Biol. 5:352, 1985) that such hybrid genes are in part transcribed by RNA polymerase II and generate abnormal transcripts.