Factors influencing alternative splice site utilization in vivo

Generation of Humanized Zebrafish Models for the In Vivo Assessment of Antisense Oligonucleotide-Based Splice Modulation Therapies

Antisense oligonucleotide (AON)-based splice modulation is the most widely used therapeutic approach to redirect precursor messenger RNA (pre-mRNA) splicing. To study the functional effect of human mutations affecting pre-mRNA splicing for which AON-based splice redirection would be a potential therapeutic option, humanized knock-in animal models are pivotal. A major limitation of using humanized animal models for this purpose is the reported poor recognition of human splice sites by the splicing machineries of other species. To overcome this problem, we provide a detailed guideline for the generation of functional humanized knock-in zebrafish models to assess the effect of mutation-induced aberrant splicing and subsequent AON-based splice modulation therapy .

Optimising the transient expression of GABA(A) receptors in adherent HEK293 cells

Owing to their therapeutic relevance, considerable efforts are devoted to the structural characterisation of membrane proteins. Such studies are limited by the availability of high quality protein due to the difficulty of overexpression in recombinant mammalian systems. We sought to systematically optimise multiple aspects in the process of transiently transfecting HEK293 cells, to allow the rapid expression of membrane proteins, without the lengthy process of stable clone formation. We assessed the impact of medium formulation, cell line, and harvest time on the expression of GABA_A receptors, as determined by [³H]muscimol binding in cell membranes. Furthermore, transfection with the use of calcium phosphate/polyethyleneimine multishell nanoparticles was optimised, and a dual vector system utilising viral enhancing elements was designed and implemented. These efforts resulted in a 40-fold improvement in GABA_A α₁β₃ receptor expression, providing final yields of 22 fmol/cm². The findings from this work provide a guide to the optimisation of transient expression of proteins in mammalian cells and should assist in the structural characterisation of membrane proteins.

Multiple activities of the human splicing factor ASF

The effects of human alternative splicing factor, ASF, on in vitro splicing of adenovirus E1A pre-mRNA were examined. E1A pre-mRNA is a complex substrate, and splicing in HeLa cell nuclear extracts produces six different RNAs using three alternative 5' splice sites and two 3' splice sites. Addition of excess ASF to splicing reactions produced a simplified splicing pattern, in which only one spliced product, 13S RNA, was detected. Inhibition of 12S and 9S splicing, which use 5' splice sites upstream of the 13S 5' splice site, extends previous observations that when multiple 5' splice sites compete for the same 3' splice site, ASF causes preferential selection of the proximal 5' splice site. However, inhibition of the other splices, which use a different upstream 3' splice site, represents a novel activity of ASF, as competition between 5' splice sites is not involved. The effect of ASF on 12S splicing was found to depend on its position relative to competing 5' splice sites, indicating that the ability of ASF to activate proximal 5' splice sites is position- but not sequence-dependent. Finally, addition of small amounts of ASF to ASF-lacking S100 extract was able to activate distal as well as proximal 5' splice sites in two of three pre-mRNAs tested, indicating that in these cases changes in the concentration of ASF alone can be sufficient to modulate alternative 5' splice site selection.

Novel splice variant of mouse insulin2 mRNA: implications for insulin expression

Insulin is a secreted peptide that controls glucose homeostasis in mammals, and insulin biosynthesis is regulated by glucose at many levels. Rodent insulin is encoded by two non-allelic genes. We have identified a novel splice variant of the insulin2 gene in mice that constitutes about 75% of total insulin2 mRNA. The alternate splicing does not alter the ORF but reduces the 5'UTR by 12 bases. A reporter gene containing the novel short 5'UTR, is more efficiently expressed in cells, suggesting that alternative splicing of insulin mRNA in mice could result in an additional level of regulation in insulin biosynthesis.

Limited complementarity between U1 snRNA and a retroviral 5' splice site permits its attenuation via RNA secondary structure

Multiple types of regulation are used by cells and viruses to control alternative splicing. In murine leukemia virus, accessibility of the 5′ splice site (ss) is regulated by an upstream region, which can fold into a complex RNA stem–loop structure. The underlying sequence of the structure itself is negligible, since most of it could be functionally replaced by a simple heterologous RNA stem–loop preserving the wild-type splicing pattern. Increasing the RNA duplex formation between U1 snRNA and the 5′ss by a compensatory mutation in position +6 led to enhanced splicing. Interestingly, this mutation affects splicing only in the context of the secondary structure, arguing for a dynamic interplay between structure and primary 5′ss sequence. The reduced 5′ss accessibility could also be counteracted by recruiting a splicing enhancer domain via a modified MS2 phage coat protein to a single binding site at the tip of the simple RNA stem–loop. The mechanism of 5′ss attenuation was revealed using hyperstable U1 snRNA mutants, showing that restricted U1 snRNP access is the cause of retroviral alternative splicing.

Production of papillomavirus-based gene transfer vectors

Papillomaviruses are a diverse group of pathogens that infect the skin and mucosal tissues of humans and various animal species. The viral genome is a circular, double-stranded DNA molecule approximately 8-kb in length. The non-enveloped papillomavirus capsid is composed of a virally encoded major coat protein, L1, and a minor coat protein, L2. L1 and L2 co-assemble when expressed in mammalian cells, and can promiscuously encapsidate essentially any <8-kb plasmid present in the cell nucleus. In the last several years, there has been rapid development of techniques for intracellular production of papillomavirus-based gene transfer vectors (also known as pseudoviruses). This unit outlines the production and propagative amplification of papillomaviral vectors. The system represents a highly tractable method for converting pre-existing mammalian expression plasmids into infectious virus stocks. The resulting vectors have utility for in vitro, as well as in vivo gene delivery applications.

RNA secondary structure and compensatory evolution

The classic concept of epistatic fitness interactions between genes has been extended to study interactions within gene regions, especially between nucleotides that are important in maintaining pre-mRNA/mRNA secondary structures. It is shown that the majority of linkage disequilibria found within the Drosophila Adh gene are likely to be caused by epistatic selection operating on RNA secondary structures. A recently proposed method of RNA secondary structure prediction based on DNA sequence comparisons is reviewed and applied to several types of RNAs, including tRNA, rRNA, and mRNA. The patterns of covariation in these RNAs are analyzed based on Kimura's compensatory evolution model. The results suggest that this model describes the substitution process in the pairing regions (helices) of RNA secondary structures well when the helices are evolutionarily conserved and thermodynamically stable, but fails in some other cases. Epistatic selection maintaining pre-mRNA/mRNA secondary structures is compared to weak selective forces that determine features such as base composition and synonymous codon usage. The relationships among these forces and their relative strengths are addressed. Finally, our mutagenesis experiments using the Drosophila Adh locus are reviewed. These experiments analyze long-range compensatory interactions between the 5' and 3' ends of Adh mRNA, the different constraints on secondary structures in introns and exons, and the possible role of secondary structures in RNA splicing.

Inhibition of SV40 large T antigen induced apoptosis by small T antigen

It is well established that the expression of simian virus 40 (SV40) early gene products causes oncogenic transformation of rodent cells. An important aspect of this process is the inactivation of the p53 and retinoblastoma (pRb) tumour suppressor proteins through interaction with the SV40 large tumour antigen (LT). In addition, the SV40 small tumour antigen (ST) may enhance LT induced transformation. Here we show that LT induces apoptotic cell death in rat embryo fibroblast (REF) cells and that ST functions to inhibit this effect by a mechanism which is different from other known anti-apoptotic proteins. Mutational analysis of LT indicates that mutants defective in the pRb-binding domain are unable to induce apoptosis whereas LT mutants defective in the p53-binding domain are still competent to induce apoptosis. Thus, interaction between LT and one or more pRb family members must occur for induction of apoptosis and that binding of p53 by LT is insufficient to inhibit LT induced apoptosis in REFs. The data presented herein suggest that the anti-apoptotic function of ST may explain, at least in part, how ST contributes to SV40 early region induced transformation of REF cells.

Naturally occurring splicing variants of the hMSH2 gene containing nonsense codons identify possible mRNA instability motifs within the gene coding region

We have identified certain unusually spliced cDNA species following PCR amplification of peripheral blood lymphocyte (PBL) mRNA from the hMSH2 gene. A naturally occurring transcript containing a nonsense codon due to the skipping of 5 exons was amplified from PBLs of several healthy individuals. A feature of this and another unusual splicing product was the presence of sequence motifs which bore significant similarity to mRNA instability determinants in the region immediately downstream of the stop codon. In particular, the rare tetranucleotide GAUG, previously identified in yeast as being of critical importance to the rapid degradation of nonsense-containing mRNAs was situated 23 base pairs downstream of the stop codon. Furthermore the region downstream of the stop codon was A:U rich and contained 2 copies of the AUUUA motif. As other forms of alternative splicing would not result in the same juxtaposition of stop codons and instability motifs, we suggest that the stop codons may have been deliberately introduced by the splicing process for their proximity to these destabilising motifs, and that splicing may play a role in channeling mRNAs into degradative pathways. These results are consistent with the hypothesis that nuclear factors may scan pre-mRNAs prior to splicing.

Genomic organization of the mouse beta 1 gene: conservation of the beta 1D but not of the beta 1B and beta 1C integrin splice variants

We have determined the genomic organization of the 3'-region of the murine beta 1 gene and cloned the murine beta 1D integrin splice variant. Overlapping genomic clones encompassing the region of the beta 1D-specific exons were isolated from a phage lambda FIXII library, mapped and partially sequenced. All of the exon-intron junctions identified in the murine beta 1 gene fit with the consensus splice donor and acceptor sequences and occur at the same positions as in their human counterparts. cDNA clones for the beta 1D integrin were isolated from a murine skeletal muscle library. The human and murine beta 1D sequences are conserved at the nucleotide (93%) and amino acid (100%) level, suggesting an important role of this muscle-specific variant throughout mammalian phylogenesis. In contrast, murine sequences for beta 1B are very different from human beta 1B at both the nucleotide as well as amino acid level. Moreover, no specific polyadenylation signal for the beta 1B variant could be identified in genomic clones, suggesting that this variant is not present in the mouse. Finally, we were not able to identify a murine beta 1C splice variant by sequencing analysis, Southern hybridization techniques or polymerase chain reaction of mRNA from platelets. These findings indicate that the beta 1B and beta 1C variants emerged relatively late in the phylogenesis of the beta 1 integrin family.

RNA structural patterns and splicing: molecular basis for an RNA-based enhancer

Efficient splicing of the 325-nt yeast (Saccharomyces cerevisiae) rp51b intron requires the presence of two short interacting sequences located 200 nt apart. We used the powerful technique of randomization-selection to probe the overall structure of the intron and to investigate its role in pre-mRNA splicing. We identified a number of alternative RNA-RNA interactions in the intron that promote efficient splicing, and we showed that similar base pairings can also improve splicing efficiency in artificially designed introns. Only a very limited amount of structural information is necessary to create or maintain such a mechanism. Our results suggest that the base pairing contributes transiently to the spliceosome assembly process, most likely by complementing interactions between splicing factors. We propose that splicing enhancement by structure represents a general mechanism operating in large yeast introns that evolutionarily preceded the protein-based splicing enhancers of higher eukaryotes.

Effects of secondary structure on pre-mRNA splicing: hairpins sequestering the 5' but not the 3' splice site inhibit intron processing in Nicotiana plumbaginifolia

We have performed a systematic study of the effect of artificial hairpins on pre-mRNA splicing in protoplasts of a dicot plant, Nicotiana plumbaginifolia. Hairpins with a potential to form 18 or 24 bp stems strongly inhibit splicing when they sequester the 5' splice site or are placed in the middle of short introns. However, similar 24 bp hairpins sequestering the 3' splice site do not prevent this site from being used as an acceptor. Utilization of the stem-located 3' site requires that the base of the stem is separated from the upstream 5' splice site by a minimum of approximately 45 nucleotides and that another 'helper' 3' splice site is present downstream of the stem. The results indicate that the spliceosome or factors associated with it may have a potential to unfold secondary structure present in the downstream portion of the intron, prior to or at the step of the 3' splice site selection. The finding that the helper 3' site is required for utilization of the stem-located acceptor confirms and extends previous observations, obtained with HeLa cell in vitro splicing systems, indicating that the 3' splice site may be recognized at least twice during spliceosome assembly.

Production of pharmaceutical proteins from transgenic animals

Different systems are being studied and used to prepare recombinant proteins for pharmaceutical use. The blood, and still more the milk, from transgenic animals appear a very attractive source of pharmaceuticals. The cells from these animals are expected to produce well-matured proteins in potentially huge amounts. Several problems remain before this process becomes used in a large scale. Gene transfer remains a difficult and costly task for farm animals. The vectors carrying the genes coding for the proteins of interest are of unpredictable efficiency. Improvement of these vectors includes the choice of efficient promoters, introns and transcription terminators, the addition of matrix attached regions (MAR) and specialized chromatin sequences (SCS) to enhance the expression of the transgenes and to insulate them from the chromatin environment. Mice are routinely used to evaluate the gene constructs to be transferred into larger animals. Mice can also be utilized to prepare amounts as high as a few hundred mg of recombinant proteins from their milk. Rabbit appears adequate for amounts not higher than 1 kg per year. For larger quantities, goat, sheep, pig and cow are required. No recombinant proteins extracted from the blood or milk of transgenic animals are yet on the market. The relatively slow but real progress to improving the efficiency of this process inclines to be reasonably optimistic. Predictive reports suggest that 10% of the recombinant proteins, corresponding to a 100 million dollars annual market, will be prepared from the milk of transgenic animals by the end of the century.

Transcription factor p91 interacts with the epidermal growth factor receptor and mediates activation of the c-fos gene promoter

Transcription factor p91 contains a SH2 domain and is activated by tyrosine phosphorylation. Here we demonstrate that epidermal growth factor (EGF) induces rapid tyrosine phosphorylation and nuclear translocation of p91. Through its SH2 domain, p91 directly interacts with the EGF receptor in a ligand-dependent manner. p91 is a necessary component of an EGF-induced DNA-binding factor that recognizes a previously identified regulatory element, SIE (c-sis-inducible element), in the c-fos gene promoter. Activated p91 stimulates SIE-dependent transcription in vitro. Cotransfection of an SIE-containing reporter with a p91 expression vector shows that p91 is a positive transcriptional regulator of the c-fos gene promoter. These studies suggest that EGF uses a direct signaling pathway to control nuclear transcriptional events.

Incomplete splicing of simian virus 40 large T antigen transcripts in a transformed mouse cell line

The SV40 large T antigen transcripts from an SV40-transformed mouse embryo fibroblast cell line (215) have been analyzed by Northern blots and by mapping and sequencing of the corresponding cDNAs. We have observed that T antigen mRNA is highly overexpressed in the 215 cells, and is mostly unspliced, but there are no sequence changes at the splice sites. However, normal amounts of wild-type T antigen are produced, suggesting that the splicing and translation of T antigen RNA is tightly controlled in these cells.

Elements of the rat tropoelastin gene associated with alternative splicing

Multiple isoforms of tropoelastin, the soluble precursor of elastin, are the products of translation of splice-variant mRNAs derived from the single-copy tropoelastin gene. Previous data had demonstrated DNA sequence heterogeneity in three domains of rat tropoelastin mRNA, indicating alternative splicing of several exons of the rat tropoelastin gene. Rat tropoelastin genomic clones encompassing the sites of alternative splicing were isolated and sequenced. Two sites of alternative splicing identified in rat tropoelastin mRNA sequences corresponded to exons 13-15 and exon 33 of the rat tropoelastin gene. Furthermore, the variable inclusion of an alanine codon in exon 16 resulted from two functional acceptor sites separated by three nucleotides. DNA sequences flanking exons subject to alternative splicing were analyzed. These exons contained splicing signals that differed from consensus sequences and from splicing signals of constitutively spliced exons. Introns immediately 5' of exons 14 and 33, for example, lacked typical polypyrimidine tracts and had weak, overlapping branch point sequences. Further, a region of secondary structure encompassing the acceptor site of exon 13 may influence alternative splicing of this exon. These results demonstrate that multiple cis-acting sequence elements may contribute to alternative splicing of rat tropoelastin pre-mRNA.

SV40 T-antigen-binding sites within the 5'-flanking regions of human U1 and U2 genes

The 5' flanking regions of the genes (U1 and U2) encoding the human U1 and U2 small nuclear RNAs (snRNAs) each contain sequences that bind specifically to the simian virus (SV40) large tumor antigen (T.Ag). Substitution of these sites with sequences that lack T.Ag-binding sites did not block accumulation of U1 or U2 snRNA in a variety of cell types, but deletion of these regions resulted in the total loss of expression. Thus, these sequences may serve only a spacing function, and the T.Ag-binding sites appear not to be necessary for expression. However, coexpression of T.Ag markedly reduced expression of a U1 gene containing a high-affinity T.Ag-binding site (from the SV40 genome) in place of the U1 T.Ag-binding site. In contrast, coexpression of T.Ag enhanced synthesis of U2, but not U1, snRNA, independent of the presence of the T.Ag-binding sites. Thus, while the consensus T.Ag-binding sites within the U1 and U2 promoter regions do not appear to influence expression, the binding of SV40 T.Ag to a high-affinity site can lead to significant repression of a strong snRNA promoter, and T.Ag can enhance expression of another in the absence of a known binding site.

Different effects of intron nucleotide composition and secondary structure on pre-mRNA splicing in monocot and dicot plants

We have found previously that the sequences important for recognition of pre-mRNA introns in dicot plants differ from those in the introns of vertebrates and yeast. Neither a conserved branch point nor a polypyrimidine tract, found in yeast and vertebrate introns respectively, are required. Instead, AU-rich sequences, a characteristic feature of dicot plant introns, are essential. Here we show that splicing in protoplasts of maize, a monocot, differs significantly from splicing in a dicot, Nicotiana plumbaginifolia. As in the case of dicots, a conserved branch point and a polypyrimidine tract are not required for intron processing in maize. However, unlike in dicots, AU-rich sequences are not essential, although their presence facilitates splicing if the splice site sequences are not optimal. The lack of an absolute requirement for AU-rich stretches in monocot introns in reflected in the occurrence of GC-rich introns in monocots but not in dicots. We also show that maize protoplasts are able to process a mammalian intron and short introns containing stem--loops, neither of which are spliced in N.plumbaginifolia protoplasts. The ability of maize, but not of N.plumbaginifolia to process stem--loop-containing or GC-rich introns suggests that one of the functions of AU-rich sequences during splicing of dicot plant pre-mRNAs may be to minimize secondary structure within the intron.

Base pairing between U2 and U6 snRNAs is necessary for splicing of a mammalian pre-mRNA

Splicing of pre-messenger RNA in eukaryotic cells occurs in a multicomponent complex termed the spliceosome, which contains small nuclear ribonucleoprotein particles (snRNPs), protein factors and substrate pre-mRNA. Assembly of the spliceosome involves the stepwise binding of snRNPs and protein factors to the pre-mRNA through a poorly understood mechanism which probably involves specific RNA-RNA, RNA-protein and protein-protein interactions. Of particular interest are the interactions between snRNPs, which are likely to be important not only for assembly of the spliceosome but also for catalysis. U1 snRNP interacts with the 5' splice site and U2 snRNP with the branch site of the pre-mRNA; both of these interactions involve Watson-Crick base pairing. But very little is known about how other factors such as the U4/U6 and U5 snRNPs reach the spliceosome and function in splicing. Here we report evidence that U6 snRNA interacts directly with U2 snRNA by a mechanism involving base-pairing, and that this interaction can be necessary for splicing of a mammalian pre-mRNA in vivo.

Developmentally regulated alternative splicing of Drosophila myosin heavy chain transcripts: in vivo analysis of an unusual 3' splice site

The 3' penultimate exon (exon 18) of transcripts from the muscle myosin heavy chain (MHC) gene of Drosophila melanogaster is excluded from mRNAs of embryonic and larval muscle, while it is included in mRNAs of adult thoracic muscles. By transforming organisms with the MHC gene 5' end, linked in-frame to the MHC gene 3' end, we were able to generate correct tissue-specific expression of this minigene and stage-specific splicing of exon 18, indicating that all the cis-acting sequences necessary for alternative splicing are contained within the construct. The 3' splice site that precedes exon 18 is unusually purine-rich, may form a stem-loop structure with the 5' splice site following exon 18, and is conserved relative to the splice site of an alternative exon of the Drosophila alkali myosin light chain gene. We converted the MHC gene 3' splice junction to a consensus splice site and also inserted the branchpoint and 3' splice site of a constitutively spliced intron in its place. These alterations had no effect on the splicing pathway in vivo, ruling out the possibility that the unusual splice junction, or secondary structures that involve this splice junction, directly regulate alternative splicing of exon 18.

Primary structure of the human splicing factor ASF reveals similarities with Drosophila regulators

We described previously the purification of a human protein, called alternative splicing factor (ASF), that can switch utilization of alternative 5' splice sites in an SV40 early pre-mRNA. We now report the isolation of a cDNA, designated ASF-1, that encodes this protein. ASF-1 consists of 248 amino acid residues, including an 80 residue RNA-binding domain at its N-terminus and a 50 residue C-terminal region that is 80% serine plus arginine. ASF-1 produced in E. coli can activate splicing in vitro and switch 5' splice-site utilization, establishing that the recombinant protein is sufficient to supply these activities. Analysis of additional cDNAs revealed that ASF pre-mRNA can itself be alternatively spliced, surprisingly, by utilization of a shared 5' splice site and two closely spaced 3' splice sites. Use of the upstream site results in a second mRNA (ASF-2) in which translation of the downstream exon occurs extensively in an alternative reading frame distinct from ASF-1.

Human pre-mRNA splicing signals

A sample of 764 pairs of human pre-mRNA exon-intron and intron-exon boundaries, extracted from the European Molecular Biology Laboratory data bank, is analyzed to provide a species-optimized characterization of donor and acceptor sites, evaluate the information content of the two signals (found to be about 8 and 9 bits respectively) and check the independent-base approximation (which holds well) and the "GT-AG" rule (to which, a few well-documented exceptions are found). No correlation is detected between the strength ("discrimination energy") of an actual donor-site signal and that of its corresponding acceptor-site counterpart, nor between that of either signal, or the cumulative strength of both, and the length of the intervening intron. The discrimination-energy distributions of the two signals are determined. Because of the large sample size and its single-species origin, the two distributions can be presumed to be representative of their underlying genomic counterparts. The size distribution of the introns shows a lower cut-off of 70 nucleotides (in essential agreement with published experimental results), and apparently no periodicities. A smaller sample of mammalian branch sites, taken from the literature, is similarly analyzed to attempt a characterization of this rather elusive signal, and provides some indication that at least part of the "long pyrimidine stretch", usually considered an integral constituent of the 3' splice signal, may be just as strongly associated with the branch site, in agreement with recent experimental observations. The usefulness of these characterizations for splice-junction searches is assessed on a test sequence.

Influences of separation and adjacent sequences on the use of alternative 5' splice sites

Single nucleotide changes to the sequence between two alternative 5' splice sites, separated by 25 nucleotides in a beta-globin gene derivative, caused substantial shifts in pre-mRNA splicing preferences, both in vivo and in vitro. An activating sequence for splicing was located. Models for the recognition by U1 small nuclear ribonucleoproteins (snRNPs) of competing 5' splice sites were tested by altering the distance separating the two sites. Use of the upstream splice site declined sharply when it was separated from the downstream (natural) site by distances of 40 nucleotides or more. This effect was reversed in vivo, but not in vitro, by altering the upstream sequence to that of a consensus 5' splice site sequence. Dilution of an extract used for splicing in vitro shifted preferences when the sites were close towards the downstream site. We conclude that the mechanism of selection depends on the distance apart of the potential splice sites and that with close sites steric interference between factors bound to both sites may impede splicing and affect splicing preferences.

Alternative splicing is an efficient mechanism for the generation of protein diversity: contractile protein genes as a model system

Alternative splicing has emerged in recent years as a widespread device for regulating gene expression and generating protein diversity. Its analysis has provided some mechanistic understanding of this form of gene regulation and, in addition, has provided new insights into some fundamental aspects of splicing. This mode of regulation is particularly prevalent in muscle cells, where genes such as troponin T are able to generate up to 64 different isoforms from a single transcriptional unit. Alternative splicing has the potential to raise the coding capacity of the small multigene families that code for the contractile proteins so that several million structurally different sarcomeres can be generated. The mammalian alpha-tropomyosin gene has proved particularly useful for the analysis of the mechanisms involved in this type of regulation. In particular, the mutually exclusive splicing of exons 2 and 3 has provided answers about the processes involved in the three main regulatory steps: (a) establishment of mutually exclusive behavior; (b) the elements involved in setting up the default pattern of splicing, and (c) the switch from the default to the regulated splicing pattern in some cell types.

Expression of CD1 in the mouse thymus

The CD1 antigens are a family of differentiation antigens found predominantly, but not exclusively, in the human thymus. Although three antigens (CD1a-c) are described by monoclonal antibodies, five genes (CD1A-E) are found in the human genome. The cloning of the mouse CD1 genes (Bradbury, A., Belt, K.T., Nery, T.M., Milstein, C. and Calabi, F., EMBO J. 1988. 7:3081) demonstrated the presence of homologues to human CD1D, but not to any of the other human CD1 genes. In this work we have examined the expression of mouse CD1D mRNA in the thymus and shown that it is predominantly cortical, as is the expression of the CD1 antigens in man. Somewhat surprisingly, we also find that most CD1D mRNA in the mouse thymus is unspliced. Despite this, we have also been able to show, using a polyclonal antiserum directed against a bacterial fusion protein, the existence of the expected protein product.

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.

Introns in the 3'-untranslated region can inhibit chimeric CAT and beta-galactosidase gene expression

The expression of a cyc::cat [cytochrome c/chloramphenicol acetyltransferase (CAT)] chimeric gene was stimulated 100-fold by the inclusion of a cyc intron in the 5'-untranslated region. In contrast, a single intron in the 3'-untranslated region was at best only slightly stimulatory, and surprisingly, inhibited expression of cat when an intron was also included in the 5'-untranslated region. This inhibition was independent of the identity of the downstream intron, occurring when either the simian virus 40 (SV40) small t intron or a cyc intron was located downstream from the cat coding region. Analysis of CAT mRNA levels, using a riboprobe spanning the 5' end of the CAT message, revealed that the stimulatory effect of a 5'-noncoding region intron were manifest at both the protein and RNA levels, whereas the inhibitory effects of 3'-noncoding region introns were detectable only at the protein level. The effects of intron position on chimeric gene expression were observed in both primate and rodent cell lines and also when the beta-galactosidase coding region was substituted for that of cat. Therefore, the common placement of an intron in the 3'-noncoding region is not the most beneficial to the expression of cyc chimeric genes. The position of introns within a transcriptional unit is a major factor to be considered when optimizing the efficiency of animal cell expression vectors.

The AU-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing

Plant cells do not in general process the introns of transcripts expressed from introduced vertebrate genes. By studying the processing of model introns in transfected plant protoplasts, we have investigated the special requirements for intron recognition by plant cells. Our results indicate that the requirements for intron recognition in plants are different from those of both metazoa and yeast. A synthetic intron of arbitrary sequence but incorporating splice site consensus sequences and a high proportion of U and A nucleotides, a characteristic feature of plant introns, was efficiently spliced in protoplasts. We have studied the effects of various sequence alterations and conclude that AU-rich sequences are necessary for intron recognition. In addition, we find that the criteria for branch site selection are relaxed, as they are in vertebrates, but a polypyrimidine tract is not necessary.

Mutually exclusive splicing of alpha-tropomyosin exons enforced by an unusual lariat branch point location: implications for constitutive splicing

Alternative splicing of alpha-tropomyosin pre-mRNA involves mutually exclusive utilization of exons 2 and 3, exon 3 being preferentially selected in most cells. This mutually exclusive behavior is enforced by absolute incompatibility between the adjacent splice sites of the two exons, due to close proximity of the exon 3 branch point to exon 2. The branch point, with an associated polypyrimidine tract, is in an unusual location, 177 nt upstream of the acceptor, only 42 nt from the exon 2 splice donor site. Splicing of exon 2 to 3 is consequently blocked prior to formation of an active spliceosome complex. This block to splicing can be relieved by insertion of spacer elements that increase the donor site-branch point separation to 51-59 nt. The unconventional relative location of the constitutive cis splicing elements therefore provides a simple mechanistic basis for strict mutually exclusive splicing. These results not only demonstrate that the branch point is not specified by proximity to the splice acceptor site, but rather suggest that it is the acceptor site which is specified relative to the branch point.

Effects of RNA secondary structure on alternative splicing of pre-mRNA: is folding limited to a region behind the transcribing RNA polymerase?

The use in vivo of an alternative 5' splice site sequestered within a short stem of potential RNA secondary structure is determined by the length of the loop. Above a threshold length of loop, the alternative site is used despite the potential structure. In contrast, the alternative site is used very little or not at all during splicing in vitro with all lengths of loop that we have tested. A model is proposed which suggests that pre-mRNA is free to fold only within a limited period after transcription.

Molecular characterization of the patatin multigene family of potato

Patatin is a family of glycoproteins that accounts for up to 40% of the total soluble protein in potato tubers. We isolated and characterized 25 patatin genomic clones. All of these exhibit different restriction patterns, but can be divided into two classes based on the presence (class II) or absence (class I) of a 22-bp sequence within the 5'-untranslated region. We determined the complete nucleotide sequence of the class-I clone PS20 and the 5'-flanking sequence of seven additional clones. The transcribed region of PS20 spans 3197 bp and is divided by six introns. The seven exons encode a transcript which is identical to the cDNA, cloned in pGM203 [Mignery et al., Nucl. Acids Res. 12 (1984) 7987-8000]. The 5'-flanking sequences of both class-I and class-II patatin genes are highly homologous up to bp position -87 and then diverge. This conserved region contains the CAAT and TATA homologies as well as a homology to the core enhancer sequence. Within a class there are additional large regions of homology, but differences exist that allow the patatin genes to be further divided into several discrete subclasses. S1 nuclease protection experiments with both class-I and class-II probes showed that class-I transcripts are the predominant species present in tubers. Class-II transcripts are present in tubers, but are 50-100-fold less abundant. In potato roots, class-II transcripts are the predominant species and few, if any, class-I transcripts are present.

Splicing of SV40 early pre-mRNA to large T and small t mRNAs utilizes different patterns of lariat branch sites

To explore the mechanism and control of alternative splicing, we have characterized the products formed by splicing of SV40 early pre-mRNA in vitro and in vivo. Large T and small t mRNAs are derived from this precursor by joining alternative 5' splice sites to a single shared 3' splice site. In contrast to pre-mRNAs studied previously, we have shown that splicing to large T RNA involves the utilization of multiple lariat branch sites, while small t splicing uses a single branch site. Interestingly, the predominant branch sites utilized in splicing of large T RNA in vitro were found to differ in nuclear extracts from HeLa and human 293 cells, correlated with previously observed differences in the ratio of large T to small t mRNAs produced in the two cell types. To test the significance of this correlation, we examined the products formed by splicing of an SV40 early precursor microinjected into X. laevis oocytes. Strikingly, both the pattern of branch sites used in large T splicing and the ratio of large T to small t mRNAs produced were found to be identical to those observed in 293 cells and extracts.

Splicing of plant pre-mRNAs in animal systems and vice versa

To investigate similarities and differences of pre-mRNA splicing between higher plants and animals, we tested whether pre-mRNAs of higher plants can be accurately spliced in animal systems, and whether an animal pre-mRNA can be spliced in plant cells. Pre-mRNAs of the maize bronze locus and oat phytochrome type 3 are accurately spliced with moderate efficiency in a human (HeLa cell) nuclear extract. The first intervening sequence (IVS1) of bean phaseolin pre-mRNA is not excised in the human nuclear extract, but is removed (although at low efficiency) in intact monkey cells. However, the IVS1 of human alpha-globin pre-mRNA is not removed in tobacco cells. Our data suggest that the mechanisms of pre-mRNA splicing are similar, but not identical, in plants and animals.