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Normal isotype switching in B cells lacking the I mu exon splice donor site: evidence for multiple I mu-like germline transcripts.

Ig class switch recombination (CSR) in activated B cells is preceded by the generation of "switch" transcripts from the heavy chain constant region (CH) genes targeted for rearrangement. Switch transcripts include a sterile "I" exon spliced onto the first CH exon. Targeted mutations disrupting the expression or splicing of I exons severely hamper CSR to all tested CH loci, except mu. However, all mu switch transcript mutations tested so far have left the I mu exon splice donor site intact. To test the possibility that the residual CSR activity in I mu mutants could be due to splicing of a truncated I mu exon, we generated new mutants specifically lacking the I mu splice donor site. Surprisingly, normal CSR was observed in the I mu splice donor mutants even in the absence of detectable spliced I mu transcripts. In a search for potential alternative sources of switch-like transcripts in the mu locus, we identified two novel exons which map just upstream of the Smu region and splice onto the C mu 1 exon. Their expression is detectable from early B cell developmental stages, and, at least in hybridomas, it does not require the Emu enhancer. These studies highlight a unique structure for the mu locus I exon region, with multiple nested switch transcript-like exons mapping upstream of Smu. We propose that all of these transcripts directly contribute to mu class switching activity.

Animals↗

Folylpoly-gamma-glutamate synthetase gene mRNA splice variants and protein expression in primary human leukemia cells, cell lines, and normal human tissues.

Folypoly-gamma-glutamate synthetase (FPGS) is essential for the cytotoxicity of "classical" antifolates and their efficacy in cancer chemotherapy. The expression of the FPGS gene appears controlled by both tissue/lineage-specific and proliferation-dependent mechanisms. Four alternative exon 1 splice variants of the FPGS gene have been described previously, but their significance in gene regulation has not been determined. Furthermore, alternative splicing of the human FPGS gene in normal or transformed cells in vivo has not been reported. We have examined the mRNA expression of these FPGS splice variants in primary human leukemia cells, cell lines, and normal human hematopoietic progenitors using reverse transcription-PCR. Specific primers were designed to amplify splice variants 1, 1A, 1B, and 1C; and full-length FPGS mRNA was amplified using primers for exons 14 and 15 at the 3' end of the gene. In this study, we demonstrate that all four alternative exon 1 variants are expressed in all primary leukemia cells and cell lines (ALL and AML), as well as in normal human hematopoietic progenitors. No significant differences in mRNA expression were detected in primary cells or cell lines for the four exon 1 splice variants. Normal circulating human lymphocytes (peripheral blood mononuclear cells) also expressed mRNA amplified from full-length FPGS and the four exon 1 splice variants, although no detectable FPGS activity was found. Using Western immunoblotting, we show that FPGS protein is expressed in these peripheral blood mononuclear cells; thus, we propose that posttranslational modification(s) is required for expression of a functional FPGS protein in human lymphohematopoietic cells. In addition, poly(A)(+) RNA from normal human adult and fetal tissues and leukemia cell lines was analyzed by Northern blot methodology. Total FPGS mRNA expression showed tissue-specificity, and higher levels were observed in human fetal tissues compared with adult tissues. The data presented herein demonstrate the existence of these FPGS mRNA splice variants in normal and transformed human hematopoietic cells and indicate that alternative splicing of the 5' end of the human FPGS gene does occur in primary cells in vivo. However, its role in regulating the expression of its mRNA remains to be determined.

Alternative Splicing↗

Novel compound heterozygous mutations for lipoprotein lipase deficiency. A G-to-T transversion at the first position of exon 5 causing G154V missense mutation and a 5' splice site mutation of intron 8.

We systematically investigated the molecular defects causing a primary LPL deficiency in a Japanese male infant (patient DI) with fasting hyperchylomicronemia (type I hyperlipoproteinemia) and in his parents. Patient DI had neither LPL activity nor immunoreactive LPL mass in the pre- and post-heparin plasma. The patient was a compound heterozygote for novel mutations consisting of a G-to-T transversion at the first nucleotide of exon 5 [+1 position of 3' acceptor splice site (3'-ass) of intron 4] and a T-to-C transition in the invariant GT at position +2 of the 5' donor splice site (5'-dss) of intron 8 (Int8/5'-dss/t(+2)c). The G-to-T transversion, although affecting the 11 nucleotide of the 3'-consensus acceptor splice site, resulted in a substitution of Gly(154) to Val (G154V; GG(716)C(-->)GTC). The mutant G154V LPL expressed in COS-1 cells was catalytically inactive and hardly released from the cells by heparin. The Int8/5'-dss/t(+2)c mutation inactivated the authentic 5' splice site of intron 8 and led to the utilization of a cryptic 5'-dss in exon 8 as an alternative splice site 133 basepairs upstream from the authentic splice site, thereby causing joining of a part of exon 8 to exon 9 with skipping of a 134-bp fragment of exon 8 and intron 8. These additional mutations in the consensus sequences of the 3' and 5' splice sites might be useful for better understanding the factors that are involved in splice site selection in vivo.

Adult↗

Purine-rich exon sequences are not necessarily splicing enhancer sequence in the dystrophin gene.

Purine-rich sequences within exons are proposed to promote proper splicing as splicing enhancers. In order to test this supposition in the dystrophin gene, which is characterized by the large size of its introns, purine-rich sequences from three exons (exons 43, 46 and 53) were examined for their splicing enhancer activity by using a Drosophila doublesex pre-mRNA. The most powerful activating effect on upstream intron splicing was seen with a sequence from exon 43. A sequence from exon 53 showed relatively low activity, whilst that from exon 46 had little effect. To characterize the splicing enhancer sequences in exons 53 and 46 further, entire exons were divided into 30nt fragments that were examined separately for their splicing enhancer activity. In exon 53, two fragments located at the 5' and 3' ends, respectively, had strong splicing enhancer activity, although they were not the most purine-rich regions of the exon. In contrast, all of the fragments derived from exon 46 had little activity. These results suggest that different exons in the dystrophin transcript are subject to different mechanisms of control by the splicing machinery.

Animals↗

Splice variants but not mutations of DNA polymerase beta are common in bladder cancer.

DNA polymerase beta (POLbeta) is a highly conserved protein that functions in base excision repair. Loss of the POLbeta locus on chromosome 8p is a frequent event in bladder cancer, and loss of POLbeta function could hinder DNA repair leading to a mutator phenotype. Both point mutations and large intragenic deletions of POLbeta have been reported from analysis of various tumor cDNAs but not from genomic DNA. We noticed that the breakpoints of the presumed rearrangements were delineated by exon-exon junctions, which could instead be consistent with alternative splicing of POLbeta mRNA. We tested the hypothesis that the reported intragenic deletion were splice variants by screening genomic DNA of human bladder tumors, bladder cancer cell lines, and normal bladder tissues for mutations or deletions in exons 1-14, exon alpha, and the promoter region of POLbeta. We found no evidence of somatic mutations or deletions in our sample set, although two polymorphisms were identified. Examination of cDNA from a subset of the original sample set revealed that truncated forms of POLbeta were surprisingly common. Forty-eight of 89 (54%) sequenced cDNA clones had large deletions, each beginning and/or ending exactly at exon-exon junctions. Because these deletions occur at exon-exon junctions and are seen in cDNA but not genomic DNA, they are consistent with alternative mRNA splicing. We describe 12 different splicing events occurring in 18 different combinations. Loss of exon 2 was the most frequent, being found in 42 of 49 (86%) of the variant sequenced clones. The splice variants appear to be somewhat more common and variable in bladder cancer cell lines and tumor tissues but occur at a high frequency in normal bladder tissues as well. We examine alternative splicing in terms of the information content of splice donor and acceptor site sequences, and discuss possible explanations for the predominant splicing event, the loss of exon 2.

Alternative Splicing↗

Development of a positive genetic selection system for inhibition of protein splicing using mycobacterial inteins in Escherichia coli DNA gyrase subunit A.

An intein-based positive genetic selection system was developed to study protein splicing and to provide a selection system with the potential for finding splicing inhibitors. Inteins can be novel antimicrobial targets when present in essential proteins since blocking splicing would kill the organism. For example, pathogenic mycobacteria encode inteins that interrupt DNA gyrase. The gyrase selection system exploits (1) splicing of inteins out of Gyrase A and (2) the dominant lethal effect of quinolone poisoning of DNA gyrase, which in turn blocks replication. The system was adapted for whole-cell high-throughput screening using green fluorescent protein as an automatable readout of viability. To demonstrate the efficacy of this system, mutations that blocked splicing of the Mycobacterium xenopi Gyrase A intein were isolated. Splicing was then assayed at a second temperature to identify inteins with a temperature-sensitive splicing phenotype. Mutations were mapped onto a structure-based sequence alignment, which led to the rational prediction of a temperature-sensitive splicing mutation. GyrA intein subdomain relationships also provided insight into intein evolution.

Amino Acid Sequence↗

Identification of cells deficient in signaling-induced alternative splicing by use of somatic cell genetics.

In recent years, a growing number of mammalian genes have been shown to undergo alternative splicing in response to extracellular stimuli. However, the factors and pathways involved in such signal-induced alternative splicing are almost entirely unknown. Here we describe a novel method for identifying candidate trans-acting factors that are involved in regulating mammalian alternative splicing, using the activation-induced alternative splicing of the human CD45 gene in T cells as a model system. We generated a cell line that stably expresses a CD45 minigene-based GFP reporter construct, such that the levels of green-fluorescent protein (GFP) expressed in the cell reflect the splicing state of the endogenous CD45 gene. Following mutagenesis of this cell line, and multiple rounds of selection for cells that displayed aberrant levels of GFP expression, we isolated several cell lines that are at least partially defective in their ability to support regulated alternative splicing of endogenous CD45 pre-mRNA in response to cell stimulation. Thus we have successfully isolated mutants in a mammalian alternative splicing pathway through use of a somatic cell-based genetic screen. This study clearly demonstrates the feasibility of using genetic screens to further our understanding of the regulation of mammalian splicing, particularly as it occurs in response to environmental cues.

Alternative Splicing↗

Cis regulating elements which control in vivo alternative splicing of the chicken beta tropomyosin primary transcript.

The beta tropomyosin gene of the chicken contains a pair of alternatively spliced mutually exclusive exons the use of which is developmentally regulated. Exon 6A is used by non muscle and undifferentiated muscle cells (myoblasts) while exon 6B is exclusively used in differentiated skeletal muscle cells. A complex array of cis acting sequence elements are involved in the regulation of this alternative splicing process. Transfection assays of quail muscle cells in culture were used to define these cis acting elements. We show that, in undifferentiated muscle cells, exon 6B is skipped as a result of a negative control on its selection while exon 6A is spliced as a default choice. We provide evidence that this negative control involves a secondary structure of the primary transcript around the 5' end of exon 6B as well as intronic sequence elements located between the branch point and the acceptor splice site of exon 6B. In differentiated muscles, both exons are accessible to the splicing machinery and the preferential use of exon 6B depends on the existence of a competition between the two exons for the selection of the flanking splice sites. In particular, we show that the donor splice site of exon 6A is a weak splice site while the branch point associated with exon 6B is a strong branch point.

Alternative Splicing↗

Trans-splicing in protozoa and helminths.

Trans-splicing is defined as the process whereby exons derived from two separately transcribed RNAs are joined together. In one type of trans-splicing, nuclear pre-mRNAs acquire their 5' terminal exon (the spliced leader) from a small spliced leader RNA (SL RNA) via an RNA processing reaction that is directly analagous to the removal of intervening sequences (cis-splicing). Such leader-addition by trans-splicing has been extensively studied in trypanosomatid protozoans and in nematodes. This review summarizes recent advances in research on trans-splicing in these two systems. Progress in elucidating functionally significant sequence elements within SL RNAs and progress in understanding the mechanism and biological role of trans-splicing is discussed.

Animals↗

A tissue-specific small nuclear ribonucleoprotein and the regulated splicing of the calcitonin/calcitonin gene-related protein transcript.

Based on a correlation between expression patterns of an abundant tissue-specific small nuclear ribonucleoprotein (N protein) and the calcitonin gene-related protein (CGRP) splicing choice, a small nuclear ribonucleoprotein (the N factor) has been hypothesized to potentially function as a trans-acting factor involved in the regulation of the alternative splicing of the calcitonin/CGRP transcript. RNA analysis indicated that most rat, human, and simian cell lines and tissues making the CGRP mRNA splicing choice expressed the N factor mRNA. These data led us to address the effect of ectopic expression of the N factor in HeLa cells, which exhibit a calcitonin splicing choice when expressing the calcitonin/CGRP gene. Expression of the N factor exerts no effect on the calcitonin/CGRP splicing choice in HeLa cells. Furthermore, several cell lines such as the human 293 cell line make the CGRP mRNA splicing choice in the absence of any detectable level of the mRNA encoding the N factor. Together, these data reveal that the N protein is neither sufficient nor required for the tissue-specific CGRP splicing decision and that the N protein is not the trans-acting factor regulating the alternative splicing of the calcitonin/CGRP gene.

Animals↗

Splice site mutations are a common cause of X-linked chronic granulomatous disease.

Chronic granulomatous disease (CGD) is characterized by the absence of a respiratory burst in activated phagocytes. Defects in at least four different genes lead to CGD. Patients with the X-linked form of CGD have mutations in the gene for the beta-subunit of cytochrome b558 (gp91-phox). We studied the molecular defect in four patients with X-linked CGD. In a fifth family, we studied the mother of a patient with X-linked CGD who had died before our investigations. Gp91-phox messenger RNA (mRNA) was reverse transcribed into cDNA and the coding region was amplified by polymerase chain reaction into three fragments. Sequence analysis showed the absence of the exon 7, 5, 3, and 2 sequences in patients 1, 2, 3, and 4, respectively. In carrier 5, we found both normal cDNA and cDNA that lacked 57 3'-nucleotides of exon 6. We analyzed the splice sites of the flanking introns of the missing exons. In patients 1, 2, and 3, we found single nucleotide substitutions within the first five positions of the down-stream 5' donor splice sites. In patient 4, a similar substitution was found at position -1 of the 3' acceptor splice site of intron 1. In carrier 5, no mutation was found in the exon 6-intron 6 boundary sequence. Instead, a single substitution was observed in exon 6 (C----A at nucleotide 633) that created a new donor splice site. Apparently, mRNA splicing occurs preferentially at this newly created splice site. We conclude that the absence of the exon sequences in the gp91-phox mRNA of these patients is due to splicing errors. Of 30 European X-linked CGD patients studied by us so far, five appear to be caused by mutations that affect correct mRNA splicing. Thus, such mutations appear to be a common cause of X-linked CGD.

Amino Acid Sequence↗

[Function of Tra2beta1 proteins in the splicing of neural-specific genes].

The in vitro studies have shown that Tra2beta1 proteins are important regulators in the alternative pre-mRNA splicing in mammalians. To date, the knowledge regarding the in vivo function of Tra2beta1 proteins, especially the function in regulating the splicing of neural-specific genes and the cell-type specificity of the functions is very limited. In the present study, the cell-type specific splicing of two neural-specific genes (GluR-B and SMN2), and the function of Tra2beta1 proteins in regulation of the splicing were studied in two types of cells (COS-1 and PFSK-1) using in vivo splicing models. The results showed that the splicing of GluR-B and SMN2 minigenes is cell-type specific, while Tra2beta1 proteins regulate the splicing of the minigenes in both cell lines in a similar pattern. It indicates that the Tra2beta1-regulated splicing of GluR-B and SMN2 minigenes regulated by Tra2beta1 is not cell-type specific.

Alternative Splicing↗

[Implication of alternative splice transcripts of caspase-3 and survivin in chemoresistance].

Recent studies have shown that resistance to apoptosis may contribute to chemoresistance. Alteration of caspases, such as caspase-3, results on decreased apoptosis. Genes of IAP (inhibitor of apoptosis proteins) family, such as survivin, were also implicated in tumor development where they are mutated or have deregulated expression. Initial studies revealed strong survivin expression in several fetal tissues and some proliferating adult tissues, whereas no survivin expression was detected in a range of adult tissues. Although the factors at the origins on survivin re-expression in tumors are still unknown, the anti-apoptotic function of survivin is mediated in part by inhibiting caspase-3 activity. Recently, functionally divergent splice variants resulting from alternative splicing, with apoptotic (for caspase-3) or anti-apoptotic (for survivin) opposite activities have been described. The alternative splice variant, caspase-3s results from exon 6 deletion and shows antagonist of apoptotic property of caspase-3. Three alternative splice variants of survivin (survivin-DeltaEx3, survivin-2B and survivin-3B) differing in their anti-apoptotic properties were reported. While the anti-apoptotic effect of survivin-DeltaEx3 is preserved, survivin-2B has lost its anti-apoptotic potential and may act as a naturally occurring antagonist of survivin and survivin-DeltaEx3. At present, little is known about properties of survivin-3B. Several evidences indicate that in several cancers, the ratio of splice variants is significantly altered, and modifications of splicing pathways have been developed for cancer treatment. Recent investigations have shown that expression of alternative splice variants of caspase-3 and of survivin were also altered in many human cancers, and that variations in their expression were associated with tumor progression and chemoresistance. In this article, we describe recent data concerning alternative splice variants of these two proteins.

Alternative Splicing↗

Alternative RNA splicing and drug target identification.

Incorporating alternative splicing content into discovery stage DNA microarray expression profiling studies fundamentally increases the relevance of the information obtained. This is because alternative splicing content addresses different parameters to those of conventional microarray content, in that it detects changes that impact the structure and function of gene products, and not simply the quantity of transcription of a given gene. Furthermore, alternative splicing has evolved not as a random process, but as a regulator of protein-protein interactions by preferentially targeting interaction domains for removal, insertion or replacement. In addition, a considerable body of literature is now available linking alternative splicing to the inheritance and pathology of diseases. Alternative splicing affects nearly every gene, with an average of three expressed protein products per gene in humans. ExonHit Therapeutics SA has recently produced the first commercial line of nucleic acid microarrays with splice event resolution that allow detection of not only the reference form of the gene, but also of all the known alternative splice forms. These microarrays enable profiling of the molecular events that are missed with conventional microarrays, and thus permit the key issues of tissue distribution and functional and pharmacological effects of alternative splicing to be addressed earlier in discovery.

Alternative Splicing↗

Splice variant of mouse Stam2 mRNA in nervous and muscle tissue contains additional exon with stop codon within region coding for VHS domain.

AIM: To analyze the alternatively spliced variant of Stam2 mRNA and determine its distribution in mouse tissues. METHODS: We identified a novel alternatively spliced exon by cloning and sequencing of Stam2 cDNA obtained from tissue samples of 3-5 months old male C57Bl/6NCrl mice. The sequence of the alternatively spliced exon was analyzed by bioinformatic tools. The tissue distribution of different Stam2 mRNA variants was determined by reverse transcription-polymerase chain reaction, and the consequences of the alternative splicing at the protein level were analyzed by western blot with the polyclonal anti-STAM2 antibody. RESULTS: The novel alternatively spliced exon 1A of mouse Stam2 gene was inserted within Stam2 coding region and it contained a stop codon. The exon did not bear similarities to any other cDNA or protein sequence in the mouse, rat, or human databases. Both mRNA variants, with and without exon 1A, were present in the cortex, hippocampus, olfactory bulb, medulla oblongata, spinal cord, cerebellum, and the skeletal and heart muscle, while the other analyzed organs contained only the variant without the additional exon. The mRNA with the included exon did not give rise to a protein form detectable by western blotting with the polyclonal anti-STAM2 antibody. CONCLUSION: The alternatively spliced exon 1A was included in mRNA splice variant present in the nervous and muscle tissues. The alternative splicing event did not have major impact on STAM2 production and functionality. It seems that exon 1A is an evolutionary new exon created by exonization of an intronic sequence.

Adaptor Proteins, Signal Transducing↗

Mining colon cancer specific alternative splicing in EST database.

Among 75218 splicing sites, 137 colon cancer specific alternative splicing isoforms were found by mining EST database. Alternative splicing database were first constructed by aligning EST to genomic sequence. Numbers of ESTs from normal or cancer colon tissue supporting splicing isoform at each splicing site were then queried and analyzed with Fisher exact test. There were 53 3' splicing, 42 5' splicing, 40 exon skipping and 2 mutual exclusive cancer specific splicing isoforms.

Alternative Splicing↗

[Pre-mRNA alternative splicing in cancer: functional impact, molecular mechanisms and therapeutic perspectives].

For most of the 25,000 human genes, the removal of introns by pre-messenger RNA splicing represents an essential step towards the production of functional messenger RNAs. Moreover, a majority of pre-messenger RNAs is alternatively spliced to yield different messenger RNAs. Cancer cells often display aberrant profiles of alternative splicing producing isoforms that can stimulate cell proliferation and migration or improve resistance to apoptosis. While mutations at splice sites or in splicing control elements have been identified, changes are also caused by alterations in the expression of proteins that affect splice site selection. Current challenges consist in documenting the functional diversity generated by alternative splicing and its contribution to different types of cancers. The development of innovative approaches aimed at reprogramming alternative splicing offers promising perspectives in cancer therapy.

Alternative Splicing↗

Repositioning of an alternative exon sequence of mouse IgM pre-mRNA activates splicing of the preceding intron.

Using a transient expression system of mouse IgM mini-gene constructs in mouse B-cell lines and in fibroblast L cell, we investigated splicing of the IgM transcript. We observed that the efficiency of splicing between exons C4 and M1 (C4-to-M1 splicing), the splicing reaction leading to the production of membrane-bound form (microns) mRNA, was drastically affected by mutations in a specific portion of the downstream exon (M2). The results show that the specific exon M2 sequence activates the C4-to-M1 splicing. This activation was not observed when splicing between exons M1 and M2 was abolished by base substitutions at the splice sites. These results indicate that positioning of the downstream exon is crucial for efficient splicing of the preceding intron.

Animals↗