Alternative splicing attenuates transgenic expression directed by the apolipoprotein E promoter-enhancer based expression vector pLIV11

The plasmid vector pLIV11 is used commonly to achieve liver-specific expression of genes of interest in transgenic mice and rabbits. Expression is driven by the human apolipoprotein (apo)E 5′ proximal promoter, which includes 5 kb of upstream sequence, exon 1, intron 1, and 5 bp of exon 2. A 3.8 kb 3′ hepatic control region, derived from a region ∼18 kb downstream of the apoE gene, enhances liver-specific expression. Here, we report that cDNA sequences inserted into the multiple cloning site (MCS) of pLIV11, which is positioned just downstream of truncated exon 2, can cause exon 2 skipping. Hence, splicing is displaced to downstream cryptic 3′ splice acceptor sites causing deletion of cloned 5′ untranslated mRNA sequences and, in some cases, deletion of the 5′ end of an open reading frame. To prevent use of cryptic splice sites, the pLIV11 vector was modified with an engineered 3′ splice acceptor site inserted immediately downstream of truncated apoE exon 2. Presence of this sequence fully shifted splicing of exon 1 from the native intron 1–exon 2 splice acceptor site to the engineered site. This finding confirmed that sequences inserted into the MCS of the vector pLIV11 can affect exon 2 recognition and provides a strategy to protect cloned sequences from alternative splicing and possible attenuation of transgenic expression.     

Organization and chromosomal localization of the human interleukin 5 receptor alpha-chain gene.

The gene for the hIL-5R alpha subunit, which is present in a single copy in the human genome, has been analysed in detail. It is located on chromosome 3 in the region 3p26. The gene organization reflects its relationship to the cytokine/haematopoietin receptor superfamily. Three introns are located in the 5' untranslated region. The subsequent exons determine the functional domains of the hIL-5R alpha protein: the signal peptide, three fibronectin type III-like (FN-like) modules, each built up by two exons, the membrane anchor and two exons forming the cytoplasmic tail, the first of which contains the proline cluster region. In addition, a specific exon generating a soluble isoform is located before the membrane anchor exon. This specific exon contains an in frame TAA stop codon, followed by a polyadenylation signal. Hence, a normal splicing event leads to a soluble IL-5R alpha variant, whereas alternative splicing is required for cell membrane anchoring. A second area of alternative splicing is found in the 5' leader sequence, and possibly relates to the presence of short open reading frames preceding the main ATG. All intron-exon junctions meet the GT-AG rule. The gene structures of all cytokine/haematopoietin receptors documented so far have also been compared with respect to intron phasing. This shows that all introns between the FN-III-like modules are of the +1 type, but in addition, splice sites within the Cys-module and WS-WS-module are invariably of the +2 and 0 type, respectively.     

The ovalbumin gene family: Structure of the X gene and evolution of duplicated split genes

The X, Y and ovalbumin genes, which are found within a 40 kb region of the chicken genome, are all expressed in oviduct under steroid hormone control, and share some sequence homologies. We have now cloned the complete X gene and have analyzed its structure. It codes for two RNA species, X and X′; both are coded by eight exons and appear to differ only by the size of their 3′ untranslated region, X′ RNA being 1400 nucleotides longer than X RNA. The striking similarity in the number and length of the exons which constitute the X, Y or ovalbumin genes establishes that they have evolved from a common ancestor gene by duplication events. Comparison of selected regions of the X and ovalbumin genes indicates that the exon sequences coding for protein and the location of the splice junctions have been well-conserved. The introns and the 3′ untranslated exonic sequences have diverged much more rapidly. Four regions of apparently unrelated repetitive sequences are found both outside the X gene and within it (in two introns and in the sequence coding for the 3′ untranslated part of X′RNA). The intragenic repetitive sequences have no counterpart in the ovalbumin and Y genes.     

Cloning and characterization of cDNAs encoding equine infectious anemia virus tat and putative Rev proteins.

We isolated and characterized six cDNA clones from an equine infectious anemia virus-infected cell line that displays a Rev-defective phenotype. With the exception of one splice site in one of the clones, all six cDNAs exhibited the same splicing pattern and consisted of four exons. Exon 1 contained the 5' end of the genome; exon 2 contained the tat gene from mid-genome; exon 3 consisted of a small section of env, near the 5' end of the env gene; and exon 4 contained the putative rev open reading frame from the 3' end of the genome. The structures of the cDNAs predict a bicistronic message in which Tat is encoded by exons 1 and 2 and the presumptive Rev protein is encoded by exons 3 and 4. tat translation appears to be initiated at a non-AUG codon within the first 15 codons of exon 1. Equine infectious anemia virus-specific tat activity was expressed in transient transfections with cDNA expression plasmids. The predicted wild-type Rev protein contains 30 env-derived amino acids and 135 rev open reading frame residues. All of the cDNAs had a frameshift in exon 4, leading to a truncated protein and thus providing a plausible explanation for the Rev-defective phenotype of the original cells. We used peptide antisera to detect the faulty protein, thus confirming the cDNA sequence, and to detect the normal protein in productively infected cells.     

Multiple messenger RNA species give rise to the structural diversity in acetylcholinesterase

Acetylcholinesterase exists predominantly as a secreted enzyme which remains cell-associated at specific extracellular locations. Its extensive structural diversity appears responsible for the unique cellular disposition of the enzyme. To examine the molecular basis of the structural divergence of acetylcholinesterase species, we hybridized total RNA from Torpedo californica electric organ with restriction fragments from a cDNA encoding the catalytic subunits of asymmetric species of acetylcholinesterase. Multiple RNA species up to 14 kilobases in length can be detected on Northern blots using a full-length cDNA for hybridization. Each of these RNA species also hybridizes with smaller restriction fragments within the open reading frame and 3'-untranslated region of the cDNA. This indicates that the entire open reading frame plus the 3'-untranslated region is contained in the large RNA species. RNase protection experiments revealed at least three points of divergence for the message species. One occurs within the COOH-terminal portion of the open reading frame at a position just 5' to the TGA stop codon. This divergence accounts for the two classes of acetylcholinesterase found in abundance in Torpedo. The site of splicing has been further defined by isolating a genomic clone containing the exon serving as the potential splice donor. We find a divergence between the cDNA and genomic DNA at the position estimated by the protection experiments. A less abundant divergence in mRNA can also be detected in the 3'-untranslated region. Another divergence occurs as a deleted sequence within the 5'-noncoding region and may be important for controlling translation efficiency. Since it is hypothesized that a single gene encodes acetylcholinesterase, the divergences in the very 3' region of the open reading frame and the 5'-noncoding region correspond to presumed splice junction boundaries where alternative RNA splicing occurs.     

Identification of a novel c-DNA overexpressed in Fanconi's anemia fibroblasts partially homologous to a putative l-3-phosphoserine-phosphatase

We applied the cDNA differential display technique (DDT) in a DNA-repair deficient cell model to isolate genes involved in dysregulation of cell proliferation and development of cancer. The comparative analysis of mRNA expression patterns of human diploid fibroblasts from Fanconi's amemia (FA) and normal phenotype led to the identification of a novel cDNA CO9. Northern blot analysis reveals that CO9 is significantly upregulated in FA fibroblasts but downregulated or absent in fibroblasts from normal donors. CO9 was also highly expressed in FA B-cells of complementation group A and in Raji cells. However, CO9 is not expressed in FA complementation groups B, C, D and E. The full-length cDNA is 840 bp long and contains an open reading frame of 216 bp (72 amino acids), which encodes for a 7.6-kDa protein. The lengths of the 5′ and 3′ untranslated region are 165 and 459 bp, respectively. The N-terminal and C-terminal nucleotide sequence of CO9 shows homology to a putative human l-3-phosphoserine phosphatase identified recently (HSPSPASE, EMBL Accession No. Y10275) but lacks a 476-bp stretch in the open reading frame. The loss of nucleotides within the open reading frame introduces a new termination codon in the CO9 cDNA along with a novel COOH terminus resulting in a new protein product. Database chromosome mapping localized CO9 to chromosome 7q 11.2. We hypothesize that CO9 represents a novel protein being a partial homologue to the l-3-phosphoserine phosphatase but with a different regulatory cell function.