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Results for “Alternative Splicing”

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PubMed1997

Complex expression pattern of the TNF region gene LST1 through differential regulation, initiation, and alternative splicing.

Recently, a novel gene, LST1, was identified in the tumor necrosis factor region of the HLA complex, 4 kb centromeric of the lymphotoxin beta gene. By analyzing several full-length cDNA clones and the genomic DNA, we identified seven exons and four introns, spanning 2.7 kb. Isolation of mouse LST1 cDNA clones established the open reading frame. LST1 transcription is characterized by four alternative transcription initiation sites and extensive alternative splicing. The derived polypeptides vary with regard to the presence of the hydrophobic N-terminus and in short internal sequences. In addition, alternative splicing results in LST1 mRNAs encoding different carboxy-terminal sequences. LST1 is predominantly transcribed in monocytes, and mRNA levels increase upon stimulation with interferon-gamma, with a concomitant change in the mRNA pattern resulting in an enhanced expression of the short LST1 transcripts. These data suggest that LST1 may have a specific role in monocytes and possibly also in T cells. Moreover, we found that the recently published cDNA 1C7 is encoded just centromeric of LST1.

Alternative Splicing↗

PubMed1999

Structural features and expression of an alternatively spliced growth factor type I receptor for follitropin signaling in the developing ovary.

The pleiotropic actions of pituitary follitropin (FSH), regulate the expression of many cell cycle genes controlling ovarian follicular development and differentiation. In this study we asked the question whether different receptor motifs are created by the alternative splicing of the single large 80-100 Kb receptor gene. A 1.2 Kb transcript identified from a cDNA library of hormone primed (immature) sheep ovaries, codes for a putative protein lacking the seven transmembrane segment. The receptor of 259 amino acids designated FSH-R3 is derived from a transcript comprising the first eight exons of the Gs coupled larger FSH receptor (R1) spliced to another DNA segment. This event produces a different carboxyl terminus at the junction creating a novel receptor motif with a single membrane spanning domain, assigning it to the growth factor type I receptor family. In transfected cells the expressed receptor localizes on the cell surface and specific antibodies directed against the unique C-terminal portion (residues 242-259) of FSH-R3 demonstrate the presence of the receptor protein in solubilized ovarian and testicular membrane preparations. FSH binding to the transfected cells induced [Ca2+]i identifying coupling of the R3 receptor to calcium signaling pathways. Thus, a growth factor type I receptor for FSH may be implicated in the growth promoting actions of FSH in the ovary. This is the first documentation of alternative splicing of a G protein coupled receptor gene creating a different signaling motif for cellular signaling.

Alternative Splicing↗

PubMed1996

cDNA cloning and characterization of A3i, an alternatively spliced rat A3 adenosine receptor variant.

A cDNA encoding variant form of the A3 adenosine (Ado) receptor was isolated from rat by reverse transcription of brain mRNA followed by PCR. The full-length receptor (A3i) cDNA encodes 337 amino acids and shares complete sequence identity with the rat A3 Ado receptor, except for the presence of a seventeen amino acid insert located in the second intracellular domain. In contrast to the rat A3 receptor, stable expression of A3i in CHO cells resulted in poor coupling to Gi proteins. Analysis of receptor transcripts by RT-PCR suggests that the A3 Ado receptor mRNAs are products of alternative splicing. Sequence analysis of A3 genomic DNA identified a 1.7 kb intron that is likely alternatively spliced to produce the A3 and A3i receptors.

Adenosine↗

PubMed2004

Myotonic dystrophy type 1 is associated with nuclear foci of mutant RNA, sequestration of muscleblind proteins and deregulated alternative splicing in neurons.

Myotonic dystrophy type 1 (DM1) is caused by expansion of a CTG repeat in the DMPK gene. In skeletal muscles, DM1 may involve a novel, RNA-dominant disease mechanism in which transcripts from the mutant DMPK allele accumulate in the nucleus and compromise the regulation of alternative splicing. Here we show evidence for a similar disease mechanism in brain. Examination of post-mortem DM1 tissue by fluorescence in situ hybridization indicates that the mutant DMPK mRNA, with its expanded CUG repeat in the 3'-untranslated region, is widely expressed in cortical and subcortical neurons. The mutant transcripts accumulate in discrete foci within neuronal nuclei. Proteins in the muscleblind family are recruited into the RNA foci and depleted elsewhere in the nucleoplasm. In parallel, a subset of neuronal pre-mRNAs show abnormal regulation of alternative splicing. These observations suggest that CNS impairment in DM1 may result from a deleterious gain-of-function by mutant DMPK mRNA.

Adult↗

PubMed1999

Cloning and expression of a short Fas ligand: A new alternatively spliced product of the mouse Fas ligand gene.

The Fas/FasL system mediates apoptosis in several different cell types, including T lymphocytes. Fas ligand (FasL), a 40-kD type II membrane protein also expressed in activated T cells, belongs to the tumor necrosis factor ligand family. We describe a new alternative splicing of mouse FasL, named FasL short (FasLs), cloned by reverse transcriptase-polymerase chain reaction. FasLs is encoded by part of exon 1 and part of exon 4 of FasL gene. The protein encoded by FasLs mRNA has a putative initiation code at position 756 and preserves the same reading frame as FasL, resulting in a short molecule lacking the intracellular, the transmembrane, and part of the extracellular domains. RNase protection and immunoprecipitation analysis showed that FasLs is expressed in nonactivated normal spleen cells and in hybridoma T cells and that it is upregulated upon activation by anti-CD3 monoclonal antibody (MoAb). Moreover, FasLs-transfected cells expressed soluble FasLs in the supernatant and became resistant to apoptosis induced by agonist anti-Fas MoAb. Thus, FasLs, a new alternative splicing of FasL, is involved in the regulation of Fas/FasL-mediated cell death.

Alternative Splicing↗

PubMed2001

Characterization of an alternatively spliced AATYK mRNA: expression pattern of AATYK in the brain and neuronal cells.

The AATYK gene encodes a tyrosine kinase whose expression is up-regulated during the apoptosis and differentiation of 32Dcl3 myeloblastic cells. Because high levels of AATYK mRNA have also been detected in the brain, and because these transcripts differ in size from that observed in the 32Dcl3 cell line, it was of interest to determine whether this gene encodes mRNAs that are alternatively spliced and whether these mRNAs are expressed in a tissue-specific manner. We have isolated a novel, alternatively spliced AATYK mRNA using cDNA library screening and RT-PCR, whose expression is readily detected in the brain but not myeloid cells. Western blot analysis revealed that the AATYK protein was expressed in virtually all regions of the adult rat brain in which neurons are present, including olfactory bulb, forebrain, cortex, midbrain, cerebellum and pons. Immunohistochemical labeling of adult brain sections showed the highest levels of AATYK expression in the cerebellum and olfactory bulb. Expression of AATYK was also up-regulated as a function of RA-induced neuronal differentiation of p19 embryonal carcinoma cells, supporting a role for this protein in mature neurons and neuronal differentiation.

Alternative Splicing↗

PubMed2002

Negative regulation of CD45 by differential homodimerization of the alternatively spliced isoforms.

The regulation of receptor-like protein tyrosine phosphatases (RPTPs) is not well understood. Although CD45 can be negatively regulated by dimerization, how dimerization is modulated is unclear. Here we show that various isoforms of CD45 differentially homodimerize in T cells. The dimerization is modulated by the sialylation and O-glycosylation of alternatively spliced CD45 exons in the extracellular domain. Thus, the smallest isoform, CD45RO--which undergoes the least extracellular sialylation and O-glycosylation--homodimerizes with the highest efficiency, resulting in decreased signaling via the T cell receptor. Because CD45 is required for T cell activation, our findings may reveal a mechanism that contributes to the termination of the primary T cell response. Our results not only demonstrate the biological significance of alternative splicing in the immune system, but also suggest a model for regulating RPTP dimerization and function.

Alternative Splicing↗

PubMed2005

Structure, alternative splicing, and expression of the human and mouse KCNIP gene family.

Potassium channel-interacting proteins (KCNIPs, also named KChIPs) modulate A-type potassium channels and favor their surface expression. In addition, KCNIPs have been shown to interact with presenilins and also to function as transcriptional repressors. Here we describe the structures and alternative splicing of the human and mouse KCNIP genes, including novel splice variants for KCNIP1, KCNIP3, and KCNIP4, and show the expression of different KCNIP mRNAs in various mouse and human tissues and brain regions by RT-PCR. Furthermore, we describe the expression of KCNIP1, KCNIP2, KCNIP3, and KCNIP4 mRNAs in the adult mouse brain with in situ hybridization and show that all KCNIP mRNAs were expressed in the neurons of the mouse brain with specific patterns for each KCNIP. Our results show that alternatively spliced KCNIP mRNAs are expressed differentially and could contribute to the diversity of functions of the KCNIP proteins.

Alternative Splicing↗

PubMed2002

Corticotropin releasing factor receptor type 1: molecular cloning and investigation of alternative splicing in the hamster skin.

The coding region of the hamster corticotropin releasing factor receptor type 1 was sequenced. Hamster gene appeared to be similar to mouse, rat, and human sequences with 95%, 94%, and 91% homology, respectively. Protein substitutions were generally found in the corticotropin releasing factor-binding domain. Thus, this domain can be more prone to mutations leading to changes in amino acid sequence. Hamster pituitary, eye, spleen, heart, skin, and four melanoma lines differentially expressed nine corticotropin releasing factor-R1 isoforms. These included the corticotropin releasing factor-R1alpha and corticotropin releasing factor-R1d homologs of human isoforms as well as e, f, h, j, k, m, and n isoforms. Corticotropin releasing factor-R1e mRNA had deletion of exons 3 and 4, CRF-R1j of exon 5, CRF-R1f of exon 11, CRF-R1k of exon 10, CRF-R1m of exons 11 and 12, and CRF-R1n of exons 10, 11, and 12. Corticotropin releasing factor-R1h had an insertion of a cryptic exon between exons 4 and 5. Reading frames of isoforms e, f, j, k, m, and h contained frameshifts, expected to produce truncated proteins. Corticotropin releasing factor-R1n isoform preserved the reading frame, but the transmembrane domains 6, 7, and one-third of the fifth were deleted. The AbC1 hamster melanoma cell line changed the pattern of alternative splicing after irradiation with ultraviolet light or induction of melanogenesis; this suggests that corticotropin releasing factor receptor alternative splicing may be regulated by common stressors, through modifications of activity and/or availability of splicing factors.

Alternative Splicing↗

PubMed2001

Genomic organization and putative promoters of highly conserved glutathione S-transferases originating by alternative splicing in Anopheles dirus.

The genomic DNA of a GST class I alternative splicing gene has been characterized from Anopheles dirus, a Thai malaria vector. This gene organization is highly conserved in An. dirus and Anopheles gambiae (aggst1alpha), with >80% nucleotide identity in the coding region. Their gene organization contains six exons for four mature GST transcripts, which share exon 1 and exon 2 but vary between four different exon 3 sequences (exon 3A-3D). The deduced amino acid sequence of the GST transcripts from these two genes also shows very high conservation, with 85-93% identity for each orthologous gene. Two putative promoters and possible regulatory elements were predicted by a combination of the TSSW and MatInspector programs. The Ad214 promoter is proposed to be involved in developmental stage regulation. The Ad2112 promoter would appear to respond to intra- or extracellular stimuli. These two Anopheline species appear to have diverged in the distant past based on gene neighbors and phylogenetic data, yet these GST genes are still conserved. Therefore it is highly probable that this GST gene organization has one or more important roles.

Alternative Splicing↗

PubMed2000

Differential expression of alternatively spliced isoforms of neuronal nitric oxide synthase (nNOS) and N-methyl-D-aspartate receptors (NMDAR) in knockout mice deficient in nNOS alpha (nNOS alpha(Delta/Delta) mice).

Recent data suggest that the neuronal isoform of nitric oxide synthase (nNOS) and glutamate receptors of the N-methyl-D-aspartate (NMDA) type are physically coupled and, hence, functionally interrelated. Several alternatively spliced isoforms of the N-methyl-D-aspartate receptor 1 (NMDAR1) subunit and the neuronal nitric oxide synthase (nNOS) are known, and recent studies have shown that a spliced C-terminal may be responsible for the coupling of NMDAR's to nNOS via its PDZ domain and the postsynaptic density protein PSD95. However, little is known about whether and to what extent changes in nNOS expression influence NMDA receptor density or function. We have therefore compared the localization of nNOS alpha, beta and gamma with that of two relevant NMDAR1 splice variants in wild-type mice versus knockout mice deficient in nNOS alpha, generated by homologous recombination with a targeted deletion of exon 2, containing one PDZ domain (nNOS alpha(Delta/Delta) mice). Whereas nNOS alpha was completely absent in nNOS alpha(Delta/Delta) mice, nNOS beta and gamma were expressed in both wild-type and knockout animals. nNOS gamma mRNA, though, was hardly detectable, if at all, mainly within the olfactory bulb, the cerebellum and mesencephalic nuclei of knockout animals. The expression of the NMDAR1-1 splice variant (without any short carboxy-terminal amino acid motif, recognized by PDZ domains) was remarkably decreased in striatal, cortical, hippocampal and cerebellar tissue in nNOS alpha(Delta/Delta) animals, but no changes in NMDAR1-4 (with an alternatively spliced C-terminal and thus with a PDZ binding motif) mRNA and protein levels were observed. While NMDAR1-4 may be related to receptor targeting and clustering to PSD95 and to nNOS, our data suggest that differences in nNOS expression obviously do not directly influence gene expression of this particular NMDAR splice variant. Otherwise, the observed diminution of NMDAR1-1 splice variant mRNA and protein levels may, at least partially, explain the decreased vulnerability of nNOS alpha(Delta/Delta) mice to glutamate-mediated neurotoxicity.

Alternative Splicing↗

PubMed1996

Modification of the alternative splicing process of testosterone-repressed prostate message-2 (TRPM-2) gene by protein synthesis inhibitors and heat shock treatment.

During the course of the study to examine the effect of cycloheximide on apoptosis-related genes, the variant rat testosterone-repressed prostate message-2 (TRPM-2) mRNA deficient of the exon 5 was found. The putative protein encoded by the variant TRPM-2 mRNA is only constituted from the N-terminal one-third portion of the ordinary TRPM-2 protein. The expression of the variant form was increased dramatically by cycloheximide treatment, while that of the ordinary form was not affected very much. The similar phenomenon was also observed by the use of other types of protein synthesis inhibitors, anisomycin and emetine. The enhancement of expression of the variant was observed in the rat treated with heat shock as well. The variant form was presumably generated by the exon skip mechanism. Systematic analyses of cycloheximide effect on the alternative splicing at various splicing junctions were performed. However, cycloheximide did not exhibit any remarkable effects on other types of alternative splicing, including exon skip in beta A4-amyloid protein precursor (APP) gene, alternative donor selection in Fas antigen gene and alternative acceptor selection in catechol O-methyltransferase (COMT) gene. These results indicated that the induction of exon skip by both protein synthesis inhibition and heat shock treatment occurs in a limited number of genes, if not only in TRPM-2.

Alternative Splicing↗

PubMed2000

Molecular cloning and expression of a functionally different alternative splice variant of prointerleukin-1alpha from the rat testis.

We report here the characterization of an alternative splice variant of prointerleukin-1alpha (proIL-1alpha), constitutively expressed by the normal adult rat testis. In addition to the classical 32K proIL-1alpha (32proIL-1alpha) messenger RNA, the testis produced a shorter variant encoding a putative protein of 24K (24proIL-1alpha). In situ hybridization demonstrated constitutive expression of the splice transcript in the seminiferous tubules. This alternative complementary DNA lacked the fifth exon, harboring the calpain cleavage site essential for generation of mature 17K IL-1alpha. This was verified by calpain treatment, producing the expected cleavage products of recombinant 32proIL-1alpha, but not of 24proIL-1alpha. Similarly, expression in COS-7 cells demonstrated processing of 32proIL-1alpha to the mature 17K form and secretion, whereas 24proIL-1alpha remained unprocessed. Both 32proIL-1alpha and 24proIL-1alpha showed a dose-dependent stimulatory effect in a thymocyte proliferation assay, although at lower potency than mature 17K IL-1alpha. In contrast, when tested on hCG-stimulated Leydig cells in vitro, a dose-dependent inhibition of testosterone production was obtained with mature 17K IL-1alpha and at a lower potency with 32proIL-1alpha, whereas 24proIL-1alpha was inactive. In conclusion, the three IL-1 bioactive proteins described here contribute to IL-1 protein heterogeneity and may serve as constitutive paracrine mediators in the testis.

Alternative Splicing↗

PubMed2006

Alternatively spliced Robo2 isoforms in zebrafish and rat.

Robo2, a member of the robo gene family, functions as a repulsive axon guidance receptor as well as a regulator of cell migration and tissue morphogenesis in different taxa. In this study, a novel isoform of the zebrafish robo2 (robo2_tv2), which included an otherwise alternatively spliced exon (CAE), has been characterized. Robo2_tv2 is expressed differentially in most non-neuronal tissues of adult zebrafish whereas robo2_tv1 expression to a great extent is restricted to the brain and eye. In zebrafish, robo2_tv2 exhibits a very-low-level basal expression starting from 1 day post fertilization until the mid-larval stages, at which time its expression increases dramatically and could be detected throughout adulthood. Our findings demonstrate that the amino acid sequence coded by CAE of the robo2 gene is highly conserved between zebrafish and mammals, and also contains conserved motifs shared with robo1 and robo4 but not with robo3. Furthermore, we provide an account of differential transcription of the CAE homolog in various tissues of the adult rat. These results suggest that the alternatively spliced robo2 isoforms may exhibit tissue specificity.

Alternative Splicing↗

PubMed1998

A family with attenuated familial adenomatous polyposis due to a mutation in the alternatively spliced region of APC exon 9.

A family is presented with attenuated familial adenomatous polyposis of variable phenotype. The clinical features range from sparse right-sided polyposis and cancer in the proximal colon at the age of 34 to pan-colonic polyposis and cancer at the age of 68. Rectal sparing is common to all affected members. Heteroduplex analysis detected bands of altered mobility in exon 9 of the APC gene in all affected family members. Subsequently, a frameshift mutation was found in the alternatively spliced region of exon 9 at codon 398 which resulted in a stop signal 4 codons downstream. Alternatively spliced transcripts that delete the mutation were readily amplified from normal colonic mucosa and therefore create a mechanism for the attenuated phenotype seen in this family.

Adenomatous Polyposis Coli↗

PubMed2005

Alternative splicing regulates the transcriptional activity of Drosophila heat shock transcription factor in response to heat/cold stress.

Heat shock transcription factor 1 (HSF1) mediates the induction of heat shock proteins in response to various types of stress. Although HSF1 activity is regulated by its post-translational modifications, alterations in mRNA expression have also been suggested. We here identified three new alternatively spliced isoforms of Drosophila HSF (dHSF) mRNA, named dHSFb, dHSFc, and dHSFd. We found that the ratio of dHSFb increases upon heat exposure, while that of dHSFd increases upon cold exposure. The dHSFc and dHSFd isoforms showed greater transcriptional activity than the other isoforms. Our findings suggest that alternative splicing regulates the transcriptional activity of dHSF.

Alternative Splicing↗

PubMed1994

An alternative splicing modifies the C-terminal end of tryptophanyl-tRNA synthetase in murine embryonic stem cells.

The cloning of murine tryptophanyl-tRNA synthetase revealed the existence of at least three messenger RNAs able to code for this enzyme. In most of the tissues tested, two major mRNA species were detected. They are produced by alternative polyadenylation and they share the same open reading frame. The deduced peptide sequence is highly homologous to bovine and human tryptophanyl-tRNA synthetases. In embryonic stem cells, a third type of mRNA was characterized. Surprisingly, this mRNA contains, at the C terminus of the open reading frame, a sequence coding for six additional amino acids. Southern blot and polymerase chain reaction analysis showed that the two open reading frames are encoded by the same gene. Thus, alternative splicing may generate two tryptophanyl-tRNA synthetase isoforms. This phenomenon is the first reported case for an aminoacyl-tRNA synthetase mRNA with two open reading frame isoforms. Moreover, to our knowledge, this is the first time that a peptide addition to the COOH terminus of a protein, by mRNA alternative splicing, is described. The extra hexapeptide, Cys-Phe-Cys-Phe-Asp-Thr COOH, resembles the consensus sequence found in C termini of Ras proteins.

Alternative Splicing↗

PubMed2001

Alternatively spliced alpha(1G) (Ca(V)3.1) intracellular loops promote specific T-type Ca(2+) channel gating properties.

At least three genes encode T-type calcium channel alpha(1) subunits, and identification of cDNA transcripts provided evidence that molecular diversity of these channels can be further enhanced by alternative splicing mechanisms, especially for the alpha(1G) subunit (Ca(V)3.1). Using whole-cell patch-clamp procedures, we have investigated the electrophysiological properties of five isoforms of the human alpha(1G) subunit that display a distinct III-IV linker, namely, alpha(1G-a), alpha(1G-b), and alpha(1G-bc), as well as a distinct II-III linker, namely, alpha(1G-ae), alpha(1G-be), as expressed in HEK-293 cells. We report that insertion e within the II-III linker specifically modulates inactivation, steady-state kinetics, and modestly recovery from inactivation, whereas alternative splicing within the III-IV linker affects preferentially kinetics and voltage dependence of activation, as well as deactivation and inactivation. By using voltage-clamp protocols mimicking neuronal activities, such as cerebellar train of action potentials and thalamic low-threshold spike, we describe that inactivation properties of alpha(1G-a) and alpha(1G-ae) isoforms can support channel behaviors reminiscent to those described in native neurons. Altogether, these data demonstrate that expression of distinct variants for the T-type alpha(1G) subunit can account for specific low-voltage-activated currents observed in neuronal tissues.

Alternative Splicing↗