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Results for “Alternative Splicing”

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PubMed1991

Hybridohistochemical demonstration of alternative splicing of the CALC-I gene.

Precursor RNA is processed to mature mRNA by excision of the noncoding introns. This process is called splicing and usually is studied by in vitro transcription experiments and by Northern blotting. The pre-mRNA of the first calcitonin gene (CALC-I) can be spliced alternatively into two different mRNAs encoding either for calcitonin or for calcitonin gene-related peptide (alpha-CGRP). The expression of CALC-I was studied by in situ hybridization in the nervous system of the rat with calcitonin-specific and CGRP-specific probes. We found evidence for alternative splicing of the pre-mRNA of CALC-I in the motor neurons of the spinal cord. alpha-CGRP mRNA was found in the nuclei and the cytoplasm of the spinal motor neurons, whereas hybridization with a calcitonin-specific probe was located strictly in the nuclei. Because no calcitonin RNA and protein was detected in the cytoplasm of the cells, we concluded that the hybridization obtained in the nucleus was the pre-mRNA encoding for alpha-CGRP.

Animals↗

PubMed2006

Our favourite alternative splice site.

Alternative splicing is a widespread mechanism in mammals that generates several mRNAs from one gene, thereby creating genetic diversity of the genome. Variant splice patterns are often specific to different stages of development or particular tissues, and alternative splicing defects are being more frequently detected in genetic diseases and cancers. The increasingly important role of alternative splicing in the function and the regulation of cellular process makes it critical to have an easy-to-use data repository for the biological and medical research communities. We have compared web resources that give access to information on alternatively spliced genes, and the FAST DB (Friendly Alternative Splicing and Transcripts DataBase) site came out as our favourite.

Alternative Splicing↗

PubMed2005

Functional manipulations of acetylcholinesterase splice variants highlight alternative splicing contributions to murine neocortical development.

Proliferation and differentiation of mammalian central nervous system progenitor cells involve concertedly controlled transcriptional and alternative splicing modulations. Searching for the developmental implications of this programming, we manipulated specific acetylcholinesterase (AChE) splice variants in the embryonic mouse brain. In wild type mice, 'synaptic' AChE-S appeared in migrating neurons, whereas the C-terminus cleaved off the stress-induced AChE-R variant associated with migratory radial glial fibers. Antisense suppression of AChE-R reduced neuronal migration, allowing increased proliferation of progenitor cells. In contrast, transgenic overexpression of AChE-R was ineffective, whereas transgenic excess of enzymatically active AChE-S or inactive AChE-Sin suppressed progenitors proliferation alone or both proliferation and neuronal migration, respectively. Our findings attribute to alternative splicing events an interactive major role in neocortical development.

Acetylcholinesterase↗

PubMed2004

A computational and experimental approach toward a priori identification of alternatively spliced exons.

Alternative splicing is a powerful means of regulating gene expression and enhancing protein diversity. In fact, the majority of metazoan genes encode pre-mRNAs that are alternatively spliced to produce anywhere from two to tens of thousands of mRNA isoforms. Thus, an important part of determining the complete proteome of an organism is developing a catalog of all mRNA isoforms. Alternatively spliced exons are typically identified by aligning EST clusters to reference mRNAs or genomic DNA. However, this approach is not useful for genomes that lack robust EST coverage, and tools that enable accurate prediction of alternatively spliced exons would be extraordinarily useful. Here, we use comparative genomics to identify, and experimentally verify, potential alternative exons based solely on their high degree of conservation between Drosophila melanogaster and D. pseudoobscura. At least 40% of the exons that fit our prediction criteria are in fact alternatively spliced. Thus, comparative genomics can be used to accurately predict certain classes of alternative exons without relying on EST data.

Alternative Splicing↗

PubMed1998

KQT2, a new putative potassium channel family produced by alternative splicing. Isolation, genomic structure, and alternative splicing of the putative potassium channels.

Potassium (K+) channels are critical for a variety of cell functions, including modulation of action potentials, determination of the testing membrane potential, and development of memory and learning. Eleven mouse cDNA clones homologous to the new human putative K+ channel (designated HNSPC, which we recently reported) were isolated from the brain cDNA libraries. All these proteins coded by the isolated cDNAs were identical from the N-terminal to the sixth transmembrane domain, but exhibited differences in the sequence and length of the C-terminal cytoplasmic region. Analyses of the mouse genomic DNAs showed that these clones originated from a single gene located on mouse chromosome 2H3-4, which proved that these clones were generated by alternative RNA splicing. Since all isoforms showed significant structural identity with KVLQT1 (64% identity in the transmembrane domains), which is known to associate with IsK, they were designated mKQT2.1-mKQT2.11. Northern blot analysis indicated that the mRNAs of the mKQT2 isoforms were exclusively expressed in the brain. In the mouse cerebellum region, the localized expression of these clones in the Purkinje cell layer and Golgi cells was shown by in situ hybridization analysis. These transcripts were also detected in the mouse embryonic developmental stage (11th, 15th and 17th day); and in particular, the mRNAs for shorter forms (mKQT2.9, mKQT2.10 or mKQT2.11) were abundantly found on the 11th day after gestation. Although these mKQT2 isoforms had the characteristic structure of voltage-gated K+ channels, functional expression of K+ currents were not detected in Xenopus oocytes.

Alternative Splicing↗

PubMed1988

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.

Humans↗

PubMed1997

Tissue-specific alternative splicing of Shaker potassium channel transcripts results from distinct modes of regulating 3' splice choice.

Alternative splicing of precursor RNA enables a single gene to encode multiple protein isoforms with different functional characteristics and tissue distributions. Differential splicing of Drosophila Shaker (Sh) gene transcripts regulates the tissue-specific expression of kinetically distinct potassium ion channels throughout development. Regulation of Sh alternative splicing is being examined in germline transformants using lacZ as a reporter gene. P-element constructs were generated in which one or both of the two mutually exclusive Sh 3' acceptor sites were positioned in the same translational reading frame as the lacZ coding sequences. The constructs were introduced into the germline and the transgenic animals examined for tissue-specific beta-galactosidase expression patterns. Some tissues exhibit "promiscuous" splicing; these tissues are competent to splice to either 3' acceptor even when both are present on the same pre-mRNA. In other tissues splice choice results from competition between the two 3' sites; these tissues can splice to either site when it is the only available 3' acceptor, but when given a choice will splice to only one of the two 3' acceptors. In some tissues, splicing occurs exclusively at only one of the 3' acceptor sites; these tissues are not competent to splice to one of the sites even if it is the only 3' acceptor present on the pre-mRNA. These results suggests that multiple, distinct regulatory modes are operating to control tissue-specific alternative splicing of Sh 3' domains and are discussed in terms of potential underlying mechanisms for regulating the tissue-specific expression of alternatively spliced genes.

Alternative Splicing↗

PubMed1998

Alternative splicing of human NrCAM in neural and nonneural tissues.

Neural cell adhesion molecule NrCAM exists in a variety of isoforms as a result of alternative splicing of individual exons during RNA processing. In this report we demonstrate that many of the alternative splicing events described for chick are conserved in man and describe a novel variant of NrCAM cDNA. Furthermore, we show that NrCAM is expressed at significant levels outside the nervous system; in particular in pancreas, adrenal glands, and placenta and that expression in both brain and other tissues is accompanied by a very variable pattern of exon utilization in fetal and adult cells.

Adrenal Glands↗

PubMed2004

Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing.

BACKGROUND: Alternative splicing contributes significantly to the complexity of the human transcriptome and proteome. Computational prediction of alternative splice isoforms are usually based on EST sequences that also allow to approximate the expression pattern of the related transcripts. However, the limited number of tissues represented in the EST data as well as the different cDNA construction protocols may influence the predictive capacity of ESTs to unravel tissue-specifically expressed transcripts. METHODS: We predict tissue and tumor specific splice isoforms based on the genomic mapping (SpliceNest) of the EST consensus sequences and library annotation provided in the GeneNest database. We further ascertain the potentially rare tissue specific transcripts as the ones represented only by ESTs derived from normalized libraries. A subset of the predicted tissue and tumor specific isoforms are then validated via RT-PCR experiments over a spectrum of 40 tissue types. RESULTS: Our strategy revealed 427 genes with at least one tissue specific transcript as well as 1120 genes showing tumor specific isoforms. While our experimental evaluation of computationally predicted tissue-specific isoforms revealed a high success rate in confirming the expression of these isoforms in the respective tissue, the strategy frequently failed to detect the expected restricted expression pattern. The analysis of putative lowly expressed transcripts using normalized cDNA libraries suggests that our ability to detect tissue-specific isoforms strongly depends on the expression level of the respective transcript as well as on the sensitivity of the experimental methods. Especially splice isoforms predicted to be disease-specific tend to represent transcripts that are expressed in a set of healthy tissues rather than novel isoforms. CONCLUSIONS: We propose to combine the computational prediction of alternative splice isoforms with experimental validation for efficient delineation of an accurate set of tissue-specific transcripts.

Alternative Splicing↗

PubMed2000

Control of hnRNP A1 alternative splicing: an intron element represses use of the common 3' splice site.

Alternative splicing of exon 7B in the hnRNP A1 pre-mRNA produces mRNAs encoding two proteins: hnRNP A1 and the less abundant A1B. We have reported the identification of several intron elements that contribute to exon 7B skipping. In this study, we report the activity of a novel element, conserved element 9 (CE9), located in the intron downstream of exon 7B. We show that multiple copies of CE9 inhibit exon 7B-exon 8 splicing in vitro. When CE9 is inserted between two competing 3' splice sites, a single copy of CE9 decreases splicing to the distal 3' splice site. Our in vivo results also support the conclusion that CE9 is a splicing modulator. First, inserting multiple copies of CE9 into an A1 minigene compromises the production of fully spliced products. Second, one copy of CE9 stimulates the inclusion of a short internal exon in a derivative of the human beta-globin gene. In this case, in vitro splicing assays suggest that CE9 decreases splicing of intron 1, an event that improves splicing of intron 2 and decreases skipping of the short internal exon. The ability of CE9 to act on heterologous substrates, combined with the results of a competition assay, suggest that the activity of CE9 is mediated by a trans-acting factor. Our results indicate that CE9 represses the use of the common 3' splice site in the hnRNP A1 alternative splicing unit.

Alternative Splicing↗

PubMed1998

Regulation of the fibronectin EDA exon alternative splicing. Cooperative role of the exonic enhancer element and the 5' splicing site.

Alternatively spliced exons generally contain weak splicing sites, and exonic and/or intronic regulatory elements recognised by trans-acting auxiliary splicing factors. The EDA exon of the fibronectin gene is a typical example of an exon bearing a purine-rich exon splicing enhancer (ESE) element recognised by members of the SR phosphoprotein family. The regulatory region that governs splicing in the human EDA exon also contains an exon splicing silencer (ESS) element. We have cloned the mouse EDA genomic region, and we show that the ESE and the ESS elements, although they have base differences, can be replaced by the human elements without significant change in the exon inclusion/exclusion ratio. This fact suggests a common splicing regulatory mechanism across species. We demonstrate in vivo the functional activity of the mouse ESE element in splicing. We also show that the trans-acting factors recognising this element cooperate with the 5' splicing site of the EDA exon to facilitate proper exon recognition. Indeed, a strong 5' splicing site overrides the ESE function in exon recognition. However, the presence of a strong 3' splicing site is not sufficient to compensate for the absence of the splicing enhancer. Our data provide in vivo evidence of the interplay between the exonic splicing regulatory elements and the splicing sites, leading finally to subtle regulation of alternative splicing.

3T3 Cells↗

PubMed1997

cDNA cloning and tissue-specific expression of a novel basic helix-loop-helix/PAS protein (BMAL1) and identification of alternatively spliced variants with alternative translation initiation site usage.

Basic helix-loop-helix (bHLH)/PAS proteins, such as Sim, act as transcriptional factors, playing a critical role in the control of central nervous system (CNS) development. To isolate novel bHLH/PAS factors in the CNS an iterative search of a database for expressed sequence tags (ESTs) resulted in the location of several bHLH/PAS protein-like sequences. The rapid amplification of cDNA end (RACE) method was applied to isolate full-length cDNAs of these ESTs. Several 5' and 3' terminal sequences were isolated using primers derived from an EST from the human brain cDNA library. The predicted novel factor polypeptide had bHLH and PAS domains that were highly homologous with those of Ah receptor nuclear translocator (Arnt) and Arnt2. Combination of the isolated cDNA fragments revealed the existence of several alternatively spliced variants. The distribution of the novel bHLH/PAS factor message was analyzed by Northern blot hybridization. This detected only one transcript, which was 2.9 kb in size. Strong hybridization was found in the brain, skeletal muscle and heart. Expression of the novel bHLH/PAS factor, brain and muscle Arnt-like protein 1 (BMAL1), was different from that of Arnt and Arnt2, suggesting that BMAL1 has a different function in the CNS and muscle than Arnt and Arnt2.

ARNTL Transcription Factors↗

PubMed2001

Lack of catalytic activity of a murine mRNA cytoplasmic serine hydroxymethyltransferase splice variant: evidence against alternative splicing as a regulatory mechanism.

Mammalian serine hydroxymethyltransferase (SHMT) is a tetrameric, pyridoxal phosphate-dependent enzyme that catalyzes the reversible interconversion of serine and tetrahydrofolate to glycine and methylenetetrahydrofolate. This reaction generates single-carbon units for purine, thymidine, and methionine biosynthesis. Cytoplasmic SHMT (cSHMT) has been postulated to channel one-carbon substituted folates to various folate-dependent enzymes, and alternative splicing of the cSHMT transcript may be a mechanism that enables specific protein-protein interactions. The cytoplasmic isozyme is expressed from species-specific and tissue-specific alternatively spliced transcripts that encode proteins with modified carboxy-terminal domains, while the mitochondrial isozyme is expressed from a single transcript. While the full-length mouse and human cSHMT proteins are 91% identical, their alternatively spliced transcripts differ. The murine cSHMT gene is expressed as two transcripts. One transcript encodes a full-length 55 kDa active enzyme (cSHMT), while the other transcript encodes a 35 kDa protein (McSHMTtr). The McSHMTtr protein present in mouse liver and kidney does not bind 5-formyltetrahydrofolate, nor does it oligomerize with the full-length cSHMT enzyme. While recombinant cSHMT-glutathione S-transferase fusion proteins form tetramers and are catalytically active, McSHMTtr-glutathione S-transferase fusion proteins are catalytically inactive, do not form heterotetramers, and do not bind pyridoxal phosphate. Analysis of the murine cSHMT crystal structure indicates that the active site lysine that normally binds pyridoxal phosphate in the cSHMT protein is exposed to solvent in the McSHMTtr protein, preventing stable formation of a Schiff base with pyridoxal phosphate. Modeling studies suggest that the human cSHMT proteins expressed from alternatively spliced transcripts are inactive as well. Therefore, channeling mechanisms enabling specific protein-protein interactions of active enzymes are not based on cSHMT alternative splicing.

Alternative Splicing↗

PubMed1998

Responsiveness of developing dental tissues to fibroblast growth factors: expression of splicing alternatives of FGFR1, -2, -3, and of FGFR4; and stimulation of cell proliferation by FGF-2, -4, -8, and -9.

To elucidate the roles of fibroblast growth factors (FGF) in tooth development, we have analyzed the expression patterns of fibroblast growth factor receptors (FGFR) in mouse teeth by in situ hybridization and studied the effects of FGF-2, -4, -8, and -9 on cell proliferation in vitro by local application with beads on isolated dental mesenchymes. mRNAs of FGFR-1, -2, and -3 were localized by probes specific for the alternative splice variants IIIb and IIIc. The expression patterns of FGFR1 -2, and -3 were completely different, and the two splicing variants of FGFR1 and 2 exhibited different expression domains. FGFR4 was not expressed in the developing teeth. The IIIb splice forms of FGFR1 and -2 were expressed in the dental epithelium during morphogenesis. The IIIc splice form of FGFR1 was expressed both in epithelium and mesenchyme whereas FGFR2 IIIc was confined to the mesenchymal cells of the dental follicle. Both splice forms of FGFR3 were expressed in dental papilla mesenchyme. None of the FGF-receptors was detected in the primary enamel knot, the putative signaling center regulating tooth morphogenesis. This may explain the fact that enamel knot cells do not proliferate, although they express intensely mitogenic FGFs. Beads releasing FGF-2, -4, -8, or -9 proteins stimulated cell proliferation in cultured dental mesenchymes. These data, together with our earlier data on FGF expression [Kettunen and Thesleff (1998): Dev Dyn 211:256-268] suggest that FGF-8 and -9 mediate epithelial-mesenchymal interactions during tooth initiation. During advancing morphogenesis FGF-3, -4, and -9 may act both on mesenchyme and epithelium. Finally, the intense expression of FGFR1 in odontoblasts and ameloblasts and FGFR2 IIIb in ameloblasts suggests that FGFs participate in regulation of their differentiation and/or secretory functions.

Alternative Splicing↗

PubMed2026

The Role of Small Segmental Duplications in Generating Identical Isoforms Through Alternative Splicing Sites.

Alternative splicing plays a crucial role in expanding proteomic diversity but can also generate identical isoforms under certain conditions. While mutually exclusive splicing of tandem exons has occasionally been reported to produce identical isoforms, the extent to which other splicing events contribute to this phenomenon remains unclear. In this study, we demonstrate that alternative 5' and 3' splice site selection can also lead to the formation of identical isoforms, providing an additional type of splicing event for functional redundancy in transcriptomes. To address this, we analyzed reference genome annotations from 15 plant species, including Arabidopsis thaliana and wheat (Triticum aestivum), obtained from the RefSeq database. Identical isoforms were computationally defined as transcripts with distinct exon-intron structures but identical coding sequences. Our analysis reveals that the majority of alternative 5' and 3' fragments originate from small segmental duplications, suggesting that sequence repetition within gene regions facilitates the emergence of such splicing patterns. We also observed differences in the annotated 5' UTRs of some identical isoforms. However, since the alternative splicing sites themselves were not located within UTRs, these differences may reflect annotation uncertainty rather than genuine AS-derived variation. Given that UTR predictions in reference databases are not always precise, such observations should be interpreted cautiously. Expression analysis using an isoform-specific k-mer approach confirmed that identical isoforms can be differentially regulated. These findings suggest that, beyond expanding protein diversity, alternative splicing can also generate redundant isoforms that are differentially expressed at the RNA level, indicating potential regulatory roles. By elucidating the structural and regulatory factors contributing to the formation and retention of identical isoforms, our study provides new insights into the evolutionary and functional significance of alternative splicing in plants.

Alternative Splicing↗

PubMed2002

L1 mediated homophilic binding and neurite outgrowth are modulated by alternative splicing of exon 2.

The neural cell adhesion molecule (CAM) L1 is a member of the immunoglobulin superfamily that has been implicated in neuronal adhesion, neurite outgrowth, and axon guidance. The clinical importance of L1 is illustrated by pathological mutations that lead to hydrocephalus, mental retardation, motor defects, and early mortality. The L1 gene is composed of 28 exons, including exons 2 and 27 that are spliced alternatively, and mutations in exon 2 are associated with severe neurological abnormalities in humans. To elucidate the role of L1 exon 2, a recombinant Fc fusion protein called Delta2L1 was constructed lacking the second exon in the extracellular domain of L1. When bound to fluorescent beads, L1 exhibited homophilic binding while Delta2L1 did not. However, L1 beads coaggregated with the Delta2L1 beads. Similarly, in cell binding studies, L1 bound to L1 and Delta2L1 did not bind to Delta2L1 but it bound moderately to L1. Given the reduced binding of Delta2L1, we tested its effect on neurons. By comparison to L1, a lower percentage of dissociated neurons extended neurites on Delta2L1, and there was a modest decrease in the length of the neurites that grew. Neurite outgrowth from reaggregated neurons was much less robust on Delta2L1 than on L1. The combined results indicate that Delta2L1 does not bind homophilically but it can interact with L1 containing exon 2. The reduced binding and neurite promoting activity of Delta2L1 provides an explanation for certain pathological mutations in L1 that lead to clinically apparent disease in the absence of the normal form of L1 in the nervous system.

Alternative Splicing↗

PubMed2000

An alternatively spliced isoform of B-Myb is a transcriptional inhibitor.

B-Myb is a highly conserved member of the Myb transcription factor family. The primary transcript of the B-myb gene is spliced alternatively in two mRNAs which either contain or lack a sequence corresponding to the so-called exon 9A of c-myb. Recent studies showed that full-length B-Myb containing the exon 9A encoded amino acids is a cell cycle regulated transcription factor whose activity is stimulated by cyclin A/Cdk 2-dependent phosphorylation at the carboxyl-terminus of B-Myb. We have now investigated in more detail the transactivation potential of the shorter isoform of B-Myb lacking exon 9A. Here, we show that B-Myb lacking exon 9A has no transactivation activity even in the presence of cyclin A. This inactivity of the shorter isoform of B-Myb is not due an improper subcelluar localization. Our work suggests that B-Myb lacking exon 9A may act as an inhibitor for full-length B-Myb mediated transactivation. Furthermore, by analysing the transactivation potential of Gal4/B-Myb fusion proteins we have identified the amino-terminal part of the exon 9A as the principal transactivation domain of full-length B-Myb. The results presented here demonstrate that B-myb encodes both an activator and an inhibitor of transcription and, thus, reveal an additional level of regulation of B-Myb activity beside the known cyclin dependent mechanisms.

Alternative Splicing↗

PubMed1993

Duplicate insulin-like growth factor-I genes in salmon display alternative splicing pathways.

Insulin-like growth factor (IGF-I) is a single chain, 70-amino acid, peptide hormone, which is essential to the process of growth and differentiation in higher vertebrates. IGF-I exhibits a very high degree of conservation throughout vertebrate evolution, and recent studies in fish have shown improved rates of growth in salmonids treated with exogenous recombinant mammalian IGF-I, implying a role for this hormone in fish similar to that in mammals. This paper reports the identification and sequencing of four different liver-derived cDNAs encoding IGF-I from chinook salmon, Oncorhynchus tshawytscha. The different cDNAs all contain sequences that encode an identical mature IGF-I protein. The differences between the four cDNAs are of two types: 1) single basepair changes and 2) additional blocks of sequence occurring at one site within the E-domain regions of three of the four cDNAs. The sequence data indicate that each of the cDNAs identified was transcribed from a different IGF-I gene, and analysis of the chinook salmon genome by Southern blotting supports the existence of four distinct IGF-I genes and suggests that there are at least two IGF-I loci in salmon. Although, analysis of total RNA from salmonid liver identifies only a single major transcript of 4200 nucleotides, polymerase chain reaction analysis suggests the presence of two structurally different salmonid IGF-I genes with the potential for multiple splicing alternatives of the IGF-I transcript.

Alternative Splicing↗