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Results for “Alternative Splicing”

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PubMed2000

Alternative splicing in 5'-untranslational region of STK-15 gene, encoding centrosome associated kinase, in breast cancer cell lines.

Centrosomes maintain genomic stability by establishing the bipolar spindles during cell division and, execute accurate segregation of chromosomes during mitosis. In this study, we have demonstrated that there are three forms of STK-15 gene in breast cancer cell lines. Alternative splice positions are located in 5'-untranslated region of STK15 gene. The results of in vitro translation experiments revealed that the alternative splicing in the 5'-untranslated region of STK15 had no effect on protein translation. The differential expression patterns of these alternatively spliced STK15 in breast cell lines and primary tumors therefore suggest that STK15 gene transcription may be differentially regulated or stabilized in these cells.

5' Untranslated Regions↗

PubMed2006

Alternative splicing controls selective trans-synaptic interactions of the neuroligin-neurexin complex.

Formation of synapses requires specific cellular interactions that organize pre- and postsynaptic compartments. The neuroligin-neurexin complex mediates heterophilic adhesion and can trigger assembly of glutamatergic and GABAergic synapses in cultured hippocampal neurons. Both neuroligins and neurexins are encoded by multiple genes. Alternative splicing generates large numbers of isoforms, which may engage in selective axo-dendritic interactions. We explored whether alternative splicing of the postsynaptic neuroligins modifies their activity toward glutamatergic and GABAergic axons. We find that small extracellular splice insertions restrict the function of neuroligin-1 and -2 to glutamatergic and GABAergic contacts and alter interaction with presynaptic neurexins. The neuroligin isoforms associated with GABAergic contacts bind to neurexin-1alpha and a subset of neurexin-1betas. In turn, these neurexin isoforms induce GABAergic but not glutamatergic postsynaptic differentiation. Our findings suggest that alternative splicing plays a central role in regulating selective extracellular interactions through the neuroligin-neurexin complex at glutamatergic and GABAergic synapses.

Alternative Splicing↗

PubMed1997

Characterization of the human apobec-1 gene: expression in gastrointestinal tissues determined by alternative splicing with production of a novel truncated peptide.

In humans, both the expression of apobec-1 and the C to U deamination of apoB mRNA are confined to the small intestine. In order to understand the tissue-restricted pattern of apobec-1 expression, we have isolated the chromosomal gene spanning the human apobec-1 locus. The human apobec-1 gene spans 18 kb and contains five exons, all of which are translated. Transcription initiation, determined by RNase protection and primer extension analyses, is localized to a single start site 34 nt upstream of the open-reading frame in exon 1. A common, but functionally silent, gene polymorphism was detected than changes Ilc80 to MCl. RNase protection and reverse-transcription PCR analysis demonstrated the presence of an exon 2-skipped form of apobec-1 mRNA that arises through use of an alternative splice acceptor. This alternative splicing causes a frame-shift that produces a novel, 36 amino acid peptide. The exon 2-skipped form accounts for approximately 50% of apobec-1 mRNA in the adult small intestine and up to 90% of apobec-1 mRNA in the developing gut. An antipeptide antibody identified the truncated protein in villus cells of the adult small intestine. These data suggest that exon 2-skipping may represent an important control mechanism regulating apobec-1 gene expression in humans.

APOBEC-1 Deaminase↗

PubMed1997

Bovine activin receptor type IIB messenger ribonucleic acid displays alternative splicing involving a sequence homologous to Src-homology 3 domain binding sites.

Activins are implicated in a variety of biological effects, particularly in reproductive processes such as embryonic development and folliculogenesis. Breakthroughs in the elucidation of the activin signal transduction mechanism were achieved with the characterization of the activin receptors, and the recent identification of cytoplasmic factors apparently involved in the signaling process. The present studies were undertaken to further analyze the activin signaling pathway. The complementary DNA coding for the bovine activin receptor type IIB (bActRIIB) was amplified by RT-PCR from corpus luteum and pituitary RNA, and cloned to characterize its role in activin signal transduction. Two complementary DNA isoforms (bActRIIB2 and bActRIIB5) were detected, coding for 512 amino acids and 498 amino acids, respectively. The shortest isoform lacked a sequence encoding a 14-amino acid stretch very rich in proline residues, located between the transmembrane region and the intracellular kinase domain. Intron sequencing and ribonuclease protection assay demonstrated that alternative splicing is responsible for the generation of these bActRIIB isoforms. This alternative splicing event is unique in that it has not been observed in other species, including the mouse, in which extensive alternative splicing of the ActRIIB messenger RNA is described. Comparison of this alternative sequence with other known proline-rich sequences showed that it has characteristics of a Src-homology 3 domain (SH3) binding site. Coprecipitation experiments have identified two proteins of 69 kDa and 71 kDa from an uterine endometrial cell line, specifically interacting with the short bActRIIB alternative proline-rich sequence. These results suggest that bActRIIB could have a protein-protein interaction, through its putative SH3 binding site, with at least two intracellular SH3-containing proteins.

Activin Receptors↗

PubMed1989

Alternative splicing of human insulin receptor messenger RNA.

The polymerase chain reaction has been used to examine alternative splicing of human insulin receptor (hINSR) mRNA. Alternative splicing of a 36 base pair exon, exon 11, generates hINSR transcripts encoding receptor isoforms which differ in sequence at the C-terminal end of the insulin-binding alpha-subunit. This process appears to be tissue-specific and, in addition, may be developmentally regulated.

Adult↗

PubMed2004

Alternatively spliced transcripts of Fas mRNAs in feline lymphoid cells.

Fas belongs to the tumour necrosis factor receptor family and transduces the death signal after binding to the Fas ligand. Five feline lymphoma cell lines were shown, by reverse transcription-polymerase chain reaction, to express six species of Fas transcripts. Based on sequence comparison of these Fas transcripts with the genomic Fas gene, five of the six transcripts were found to be generated through alternative splicing and to encode five different Fas proteins lacking the transmembrane domain. We also detected such alternatively spliced transcripts in primary tumour tissues from cats with naturally occurring lymphoma. These results suggest a possible association of the alternatively spliced Fas variants with the pathogenesis of feline lymphoma.

Alternative Splicing↗

PubMed1986

Alternative splicing in the mouse H-2Kd gene is not necessary for the classical Kd antigen function.

The mouse H-2Kd gene gives rise to several transcripts by alternative splicing. In addition to encoding the known Kd antigen, it could thus encode at least one minor hypothetical Kd-like molecule, with a distinct NH2 terminus. The existence of this "24" product can be inferred from a cDNA clone which was previously isolated. We have engineered both this cDNA and its canonical counterpart into a eukaryotic expression vector. After transfer of these constructs into mouse fibroblasts, we obtained cells expressing either one of the transcripts, but not both. In cytotoxicity tests, we found no expression of the "24" product on the cell surface, nor did we obtain any clue concerning its function. In contrast, cells which express Kd antigen, but none of the possible Kd-like molecules produced by alternative splicing, were functional in all aspects examined. We conclude that alternative splicing does not contribute to the known function of the Kd antigen.

Animals↗

PubMed1996

New proteins in the rat CYP2B subfamily: presence in liver microsomes of the constitutive CYP2B3 protein and the phenobarbital-inducible protein product of alternatively spliced CYP2B2 mRNA.

The rat CYP2B gene subfamily includes CYP2B1, CYP2B2 and CYP2B3. Translation of an alternatively spliced hepatic CYP2B2 mRNA would generate a CYP2B2 variant, CYP2B2v, having eight additional amino acid residues inserted between CYP2B2 positions 274 and 275. The presence of CYP2B3 and CYP2B2v in rat liver has yet to be demonstrated. cDNA expression vectors were obtained for CYP2B1, CYP2B2, CYP2B3 and CYP2B2v. All four proteins react with an anti-CYP2B1 antibody and can be resolved by SDS-PAGE. A CYP2B3-specific polyclonal antibody raised against an undecapeptide (SPVDPNTIDMT) from near the C-terminus of CYP2B3 detected a constitutive protein on immunoblots of rat liver microsomes, thus demonstrating that the CYP2B3 mRNA is translated in the liver. Similarly, a CYP2B2v-specific polyclonal antibody was raised against a peptide containing the eight additional amino acid residues (VSPAWMRE) predicted to be present in the CYP2B2v protein. It detected a phenobarbital- and Aroclor 1254-inducible protein in rat liver microsomes. Microsomes of Ad293 cells expressing cDNAs for CYP2B2 and CYP2B2v were used to metabolize 7,12-dimethylbenz[a]anthracene (DMBA), and the metabolites produced were compared with those generated by microsomes of cells expressing CYP2B1 cDNA. CYP2B2v had activity similar to that of CYP2B2 for DMBA metabolism. Both CYP2B2 forms preferentially catalyzed 12-hydroxylation, whereas CYP2B1 preferred 7-hydroxylation and exhibited turnover that was strongly suppressed as previously reported. These results demonstrate the existence in rat liver of two new CYP2B proteins: CYP2B3, the major constitutive CYP2B form, and CYP2B2v, which represents a rare case of non-aberrant alternative splicing among xenobiotic-metabolizing P450s.

9,10-Dimethyl-1,2-benzanthracene↗

PubMed2004

Stress-induced alternative splicing of acetylcholinesterase results in enhanced fear memory and long-term potentiation.

Stress insults intensify fear memory; however, the mechanism(s) facilitating this physiological response is still unclear. Here, we report the molecular, neurophysiological and behavioral findings attributing much of this effect to alternative splicing of the acetylcholinesterase (AChE) gene in hippocampal neurons. As a case study, we explored immobilization-stressed mice with intensified fear memory and enhanced long-term potentiation (LTP), in which alternative splicing was found to induce overproduction of neuronal 'readthrough' AChE-R (AChE-R). Selective downregulation of AChE-R mRNA and protein by antisense oligonucleotides abolished the stress-associated increase in AChE-R, the elevation of contextual fear and LTP in the hippocampal CA1 region. Reciprocally, we intrahippocampally injected a synthetic peptide representing the C-terminal sequence unique to AChE-R. The injected peptide, which has been earlier found to exhibit no enzymatic activity, was incorporated into cortical, hippocampal and basal nuclei neurons by endocytosis and retrograde transport and enhanced contextual fear. Compatible with this hypothesis, inherited AChE-R overexpression in transgenic mice resulted in perikaryal clusters enriched with PKCbetaII, accompanied by PKC-augmented LTP enhancement. Our findings demonstrate a primary role for stress-induced alternative splicing of the AChE gene to elevated contextual fear and synaptic plasticity, and attribute to the AChE-R splice variant a major role in this process.

Acetylcholinesterase↗

PubMed2004

Human tra2-beta1 autoregulates its protein concentration by influencing alternative splicing of its pre-mRNA.

HTRA2-BETA1 is an SR-like protein that regulates alternative splice site selection in a concentration-dependent manner. Its proper concentration is important as several pathological states are associated with its change. We investigated the mechanism that controls the cellular HTRA2-BETA1 concentration and found it utilizes a negative feedback loop to regulate the splicing of its exon 2. TRA2-BETA1 binds to four enhancers present in exon 2, which activates its inclusion. Inclusion of exon 2 generates mRNAs that are not translated into proteins. Mutations of exon 2 enhancers demonstrate that TRA2-BETA1 binds a degenerate sequence GHVVGANR, which is found more frequently in exons than in introns. Hyperphosphorylation of TRA2-BETA1 strongly reduces its binding to RNA. Presence of the CLK2 kinase prevents the usage of exons 2 and 3, generating the htra2-beta3 mRNA. The resulting HTRA2-BETA3 protein lacks the first RS domain of HTRA2-BETA1, is expressed in several tissues and has no influence on tra2-beta splice site selection. HTRA2-BETA1 interacting proteins promote exon 2 skipping by sequestering it, which upregulates the HTRA2-BETA1 protein synthesis. We propose that the regulation of the tra2-beta pre-mRNA alternative splicing provides a robust and sensitive molecular sensor that measures the ratio between HTRA2-BETA1 and its interacting proteins.

Alternative Splicing↗

PubMed1999

Asthmatic airway biopsy specimens are more likely to express the IL-4 alternative splice variant IL-4delta2.

BACKGROUND: The human IL4 gene, has been shown to express the alternatively spliced messenger (m)RNA IL-4delta2. IL-4delta2 is missing the entire sequence from exon 2 and has been identified as an IL-4 receptor antagonist. OBJECTIVE: We sought to distinguish IL-4 and IL-4delta2 mRNA in respiratory tract tissue for the first time. METHODS: A novel competitive PCR assay was established with primers designed on either side of the alternative splice junction of the IL4 gene, allowing the simultaneous quantitation of both IL-4 and IL-4delta2 mRNA from one reaction. RESULTS: IL-4 and IL-4delta2 were differentially expressed in 4 nasal polyps. No difference was seen in endobronchial biopsy specimens for IL-4 mRNA expression between control subjects (median, 2.8 x 10(2) copies/microg RNA; range, 0-3.7 x 10(3) copies/microg RNA) and asthmatic subjects (median, 1.4 x 10(2) copies/microg RNA; range, 0-4.7 x 10(2) copies/microg RNA). However, significantly more asthmatic subjects (6 of 9) than control subjects (1 of 7) expressed IL-4delta2 (P =. 036). Expression of IL-4 variants was unaffected by atopic status. CONCLUSIONS: Given that IL-4delta2 is an IL-4 receptor antagonist, these results indicate that it is crucial to be able to distinguish IL-4delta2 from IL-4 when assessing IL4 gene expression. Increased expression of IL-4delta2 in stable asthmatic subjects suggests that the balance of IL-4 and IL-4delta2 may modulate asthmatic inflammation.

Adult↗

PubMed2002

Alternative splicing of brain-specific PTB defines a tissue-specific isoform pattern that predicts distinct functional roles.

Splicing of neural-specific exons is differentially regulated in neuronal and non-neuronal cells. The polypyrimidine tract binding protein (PTB) has been implicated as a negative regulator for exon splicing, whereas the brain-specific homolog of PTB, termed nPTB, promotes exon splicing exclusively in neurons. We have now isolated a novel mRNA splice variant of nPTB from non-neuronal cells. In contrast to the neural nPTB transcript, the expression of this novel isoform was absent from brain tissue and was generated in non-neuronal cells by alternative splicing to include five additional amino acid residues encoded by exon 9. In addition, we identified a brain-specific transcript containing a novel, alternatively spliced, internal exon 10. The exclusion of this 34-nucleotide exon 10 in non-neuronal tissues generates a premature termination codon and results in the truncation of the open reading frame. Our findings suggest that alternative splicing of nPTB has an important role in regulation of tissue-specific gene expression and thus in the functional activity of nPTB in neuronal and non-neuronal cells.

Alternative Splicing↗

PubMed2001

Antagonistic effects of T-Ag and VP16 reveal a role for RNA pol II elongation on alternative splicing.

Here we investigate the promoter control of alternative splicing by studying two transcriptional activators on templates under replicating conditions. SV40 large T-antigen (T-Ag) activates template replication only 2-fold but transcription 25-fold. T-Ag-mediated replication, reported to inhibit RNA polymerase II elongation, provokes a 10- to 30-fold increase in the inclusion of the fibronectin EDI exon into mature mRNA. The T-Ag effect is exon specific, occurs in cis and depends strictly on DNA replication and not on cell transformation. VP16, an activator of transcriptional initiation and elongation, has a similar effect on transcription but the opposite effect on splicing: EDI inclusion is inhibited by 35-fold. VP16 completely reverts the T-Ag effect, but a VP16 mutant with reduced elongation ability provokes only partial reversion. Both T-Ag and VP16 promote conspicuous co-localization of mRNA with nuclear speckles that contain the SR protein SF2/ASF, a positive regulator of EDI inclusion. Therefore, we conclude that co-localization of transcripts and speckles is not sufficient to stimulate EDI inclusion.

Alternative Splicing↗

PubMed1997

The alternatively spliced domains EIIIB and EIIIA of human fibronectin affect cell adhesion and spreading.

Fibronectin has a complex pattern of alternative splicing at the pre-mRNA level leading to the expression of different isoforms. The alternatively spliced domains EIIIB and EIIIA are known to be prominently expressed during development and wound healing. While the other spliced domain (CS-segment) is known to promote cell adhesion in a cell type specific manner, the biological functions of the spliced domains EIIIB and EIIIA are not well understood. In the present study, we have prepared expression proteins of specific domains of human fibronectin using a prokaryotic expression system and used the purified fragments to test their ability to support adhesion and spreading of cultured cells. Fragments from type-III domains #7 to #12 were prepared in various combinations to include or exclude the spliced domains EIIIB and EIIIA. The results indicate that cultured NIL fibroblasts adhere to many of the fragments tested. However, the cell adhesion and spreading are enhanced, especially at lower concentrations, to fragments including the domain EIIIB. The inclusion of domain EIIIA led to a decrease in the adhesion of cells and those that adhered did not spread well. When tested in a centrifugal cell adhesion assay, fragments including domain EIIIB resisted the detaching forces and stayed adhered. Fragments that included domain EIIIA were unable to resist the detaching centrifugal forces to the same extent as the fragments that included domain EIIIB alone. These results suggest that the spliced domain EIIIB may be serving important biological functions in enhancing cell adhesion and spreading. This is likely to be mediated by conformational effects because domain EIIIB alone neither exhibited any adhesive activity nor competed in inhibiting adhesion to fragments #7-10.

Actins↗

PubMed1997

Alternative splicing of cyclin transcripts in maize endosperm.

Cyclins are the regulatory subunits of cyclin-dependent protein kinases. In investigations of the expression of a cyclin gene during maize endosperm development, we detected a cyclin transcript with a 63-bp deletion in the region encoding the conserved 'cyclin box' where cyclin interacts with p34cdc2, the catalytic domain of the cyclin-dependent protein kinase. Analysis of cDNA and genomic sequences, and other observations, indicated that the deletion was caused by alternative splicing of a retained intron in the normally spliced transcript. Whereas the normally spliced cyclin RNA was mitotically functional, as indicated by its ability to promote maturation of Xenopus oocytes, the alternatively spliced transcript was unable to promote maturation. In addition to maize endosperm, the alternatively spliced cyclin was detected in apical meristem, mature leaf, root tip and mature root.

Alternative Splicing↗

PubMed2001

Analysis of smu-1, a gene that regulates the alternative splicing of unc-52 pre-mRNA in Caenorhabditis elegans.

Mutations in the smu-1 gene of Caenorhabditis elegans were previously shown to suppress mutations in the genes mec-8 and unc-52. mec-8 encodes a putative RNA binding protein that affects the accumulation of specific alternatively spliced mRNA isoforms produced by unc-52 and other genes. unc-52 encodes a set of basement membrane proteins, homologs of mammalian perlecan, that are important for body wall muscle assembly and attachment to basement membrane, hypodermis, and cuticle. We show that a presumptive null mutation in smu-1 suppresses nonsense mutations in exon 17 but not exon 18 of unc-52 and enhances the phenotype conferred by an unc-52 splice site mutation in intron 16. We have used reverse transcription-PCR and RNase protection to show that loss-of-function smu-1 mutations enhance accumulation in larvae of an alternatively spliced isoform that skips exon 17 but not exon 18 of unc-52. We have identified smu-1 molecularly; it encodes a nuclearly localized protein that contains five WD motifs and is ubiquitously expressed. The SMU-1 amino acid sequence is more than 60% identical to a predicted human protein of unknown function. We propose that smu-1 encodes a trans-acting factor that regulates the alternative splicing of the pre-mRNA of unc-52 and other genes.

Alternative Splicing↗

PubMed2005

Distinct turnover of alternatively spliced isoforms of the RET kinase receptor mediated by differential recruitment of the Cbl ubiquitin ligase.

Alternative splicing of transcripts encoding the RET kinase receptor leads to isoforms differing in their cytoplasmic tail. Although in vitro studies have demonstrated a higher transforming activity of the long RET isoform (RET51), only the short isoform (RET9) can rescue the effects of a RET null mutation in the enteric nervous system and kidney development. The molecular basis underlying the distinct functions of the two RET isoforms is not understood. Here we demonstrated that activated RET51 associated more strongly with the ubiquitin ligase Cbl than did RET9, leading to increased ubiquitylation and faster turnover of RET51. The association of Cbl with RET was indirect and was mediated through Grb2. A constitutive complex of Grb2 and Cbl could be recruited to both receptor isoforms via docking of Shc to phosphorylated Tyr-1062 in RET. A mutant Shc protein unable to recruit the Grb2.Cbl complex decreased the turnover and prolonged the half-life of RET9, thus ascribing a previously unknown negative role to the Shc adaptor molecule. In addition, phosphorylation of Tyr-1096, which is present in RET51 but absent in RET9, endowed the longer isoform with a second route to recruit the Grb2.Cbl complex. These findings establish a mechanism for the differential down-regulation of RET9 and RET51 signaling that could explain the apparently paradoxical activities of these two RET isoforms. More generally, these results illustrate how alternative splicing can regulate the half-life and function of a growth factor receptor.

Adaptor Proteins, Signal Transducing↗

PubMed1993

Alternative splicing in the fragile X gene FMR1.

The FMR1 gene, associated with fragile X syndrome, has recently been cloned and the sequence of partial cDNA clones is known. We have determined additional cDNA sequences both at the 5' and 3' end. We have characterized the expressed gene by means of RT-PCR in various tissues and have found that alternative splicing takes place in the FMR1 gene, which does not seem to be tissue specific. When the different alternative splicing events are combined, 12 distinct mRNA products could result from FMR1 expression in each tested tissue. In all these transcripts the open reading frame is maintained until the same stop codon. At the 3' end alternative use of polyadenylation signals is found. The alternative splicing allows functional diversity of the FMR-1 gene. Whether all the possible proteins will be synthesized and whether they will be functionally active has to be determined.

Alternative Splicing↗