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Results for “Alternative Splicing”

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PubMed2004

Alternative spliced variants of the alpha-methylacyl-CoA racemase gene and their expression in prostate cancer.

Alpha-methyacyl-CoA racemase (AMACR), a mitochondrial and peroxisomal enzyme essential in lipid metabolism, is overexpressed in prostate cancer. Two different AMACR transcripts (designated IA and IIA), each derived from five exons, have been reported. AMACR IA, the most abundant form, encodes a 382-amino acid protein (Mw 42 kDa, pI 6.07). AMACR IIA contains an alternative fifth exon that has extensive homology to the human fumarate hydratase (FH) and encodes a 288-amino acid protein (Mw 32 kDa, pI 9.6). Here we report additional variants of IA and IIA whereby the transcripts lack exon 3 and are designated as IB (Mw 22 kDa, pI 10.31) and IIB (Mw 31 kDa, pI 9.44). Due to a frameshift, the alternative fifth exon in the IIA transcript encodes a polypeptide that differs from FH. In contrast, the IIB transcript, generated as a result of the dual alternative splicing events, encodes a polypeptide homologous with a highly conserved region of FH. We also identified a shorter variant form of IIA (IIAs, Mw 28 kDa, pI 9.65), which lacks the 5' half of the alternative fifth exon. The carboxy termini of all five gene products differ as a result of the alternative splicing events. In prostate tumor tissues that overexpressed AMACR, both the A and B forms were overexpressed, suggesting coregulation. Only the predominant AMACR IA has an acidic pI and contains the previously identified peroxisomal targeting signal (PTS1) peptide, while the other four variants are basic proteins that lack the peroxisomal targeting signal peptide. These observations have implications for the cellular localization and function of these AMACR variants.

Alternative Splicing↗

PubMed2000

Identification of a family of alternatively spliced mRNA species of angiopoietin-1.

Angiopoietin-1 (Ang-1) is required for developing vessels, and its absence leads to defects in vessel remodeling. Ang-1 has been identified as the ligand for the tyrosine kinase receptor Tie-2, which is expressed specifically on endothelial cells and early hematopoietic cells. In studying the role of Tie-2 and Ang-1 in megakaryocytopoiesis, 3 alternatively spliced species of Ang-1 mRNA (Ang-1.3 kb, Ang-0.9 kb, and Ang-0.7 kb) were identified in addition to the full-length Ang-1 (Ang-1.5 kb), in the megakaryocyte cell line CHRF by reverse transcription-polymerase chain reaction (RT-PCR), and then cloned and sequenced. The expression of 3 alternatively spliced isoforms of Ang-1 was confirmed by RT-PCR using specific primer pairs derived from junction sites and the 3' end of Ang-1 cDNA, and it was further demonstrated by nuclease protection assay, Northern blotting, and immunoblotting in CHRF cells. Expression of the Ang-1.3 kb isoform was also detected in human primary fibroblast cell line FS4, breast cancer cell line MDAMB-468, and CD34(+)CD41(+) cells of fetal liver and platelets. The function of the 1.5-kb, 1.3-kb, and 0.9-kb isoforms was examined. Recombinant proteins Ang-1.5 and 0.9 kb bind strongly to the recombinant Tie-2 receptor (Tie-2-Fc), whereas the 1.3-kb isoform does not. The Ang-1.3 kb isoform binds to the 1.5-kb isoform. Ang-1. 5 kb, but not the 1.3-kb and 0.9-kb isoforms, induces tyrosine phosphorylation of Tie-2 in human umbilical vein endothelial cells. These data suggest that isoforms 1.3 kb and 0.9 kb could serve as dominant negative molecules for the full-length Ang-1. The possible involvement of the newly identified Ang-1 isoforms in angiogenesis and in growth and differentiation of hematopoietic progenitor cells provides a greater complexity to these processes. (Blood. 2000;95:1993-1999)

Alternative Splicing↗

PubMed2000

Identification of an alternatively spliced form of the Tat interactive protein (Tip60), Tip60(beta).

Tip60 was originally isolated as a Tat interactive protein. It was subsequently shown that Tip60 had histone acetyltransferase (HAT) activity. In studies to understand gene-expression regulation that might involve HAT activity, we PCR-amplified Tip60 from a human heart marathon-ready cDNA library. As a result, we identified an alternatively spliced form of Tip60, Tip60beta (we refer to the previously cloned Tip60 as Tip60alpha). Tip60beta cDNA is slightly smaller than Tip60alpha, and sequencing indicates that there is a deletion of 156 bp in the coding region of the gene. The predicted Tip60beta protein therefore lacks 52 amino acids when compared with Tip60alpha. The Tip60alpha gene is encoded by 14 exons, and Tip60beta is an alternatively spliced form resulting from the exclusion of exon 5 during the splicing process. Exon 5 encodes a proline-rich region that is known to be important for protein-protein interaction. Tip60beta is expressed in a variety of human tissues and cell lines, and the protein is present in both the nucleus and cytoplasm in contrast to Tip60alpha, which is entirely nuclear. The results suggest that Tip60beta may have functions additional to those of Tip60alpha in cells and tissues.

Acetyltransferases↗

PubMed2001

Regulation of CD40 function by its isoforms generated through alternative splicing.

CD40 is a member of the tumor necrosis factor receptor superfamily. The interaction between CD40 and CD40 ligand (CD154) activates NF-kappa B, Jun N-terminal kinase, and Janus kinase/signal transducers and activators of transcription pathways and promotes B cell growth, differentiation, and survival as well as IL-12 production in macrophages and dendritic cells. We demonstrate here the existence of multiple isoforms of CD40 mRNA generated by alternative splicing and show that their expression is regulated differentially in activated macrophages and dendritic cells. Pre-CD40 RNA is spliced preferentially out to signal-transducible CD40 mRNA in the early stage of activation; half of the CD40 mRNA is replaced by the signal-nontransducible CD40 mRNAs in the later stages (24 h). Using IL-12 p40 gene expression as a reporter for CD40 signaling, we show that three of the alternative isoforms can disable signaling through CD40. The major alternative isoform lacks the membrane-associated endodomain and seems to reduce the amount of the signal-transducible form available on the cell surface. It would seem, therefore, that CD40 expression is controlled by posttranscriptional and posttranslational regulation through alternative splicing. Modulation of isoform expression may provide a mechanism by which cells regulate their susceptibility to CD40L signaling.

Alternative Splicing↗

PubMed1998

Synthesis of turkey Pit-1 mRNA variants by alternative splicing and transcription initiation.

The gene encoding turkey Pit-1/GHF-1 (tPit-1) spans approximately 12 kilobases (kb) and consists of 7 exons. One exon, which is located between exons 2 and 3, is designated exon 2a and codes for 38 amino acids not found in mammalian Pit-1. Because all tPit-1 variants contain exon 2a, they are denoted with an asterisk (*) to distinguish them from comparable mammalian Pit-1s. Three tPit-1 variants are generated by alternative splicing and transcription initiation. Splicing of exon 1 to an alternative acceptor splice site in exon 2 results in a 28 amino acid insertion in tPit-1beta* relative to tPit-1*. A transcript unique to the turkey has been identified by RT-PCR and RNase mapping. This transcript, designated tPit-1W*, arises following transcription initiation upstream of the alternative acceptor splice site in exon 2. In turkey pituitary, the mRNA for the tPit-1* variant is the most abundant, the tPit-1W* variant is intermediate, and the tPit-1beta* variant is the least abundant.

Alternative Splicing↗

PubMed1988

Multiple human tyrosine hydroxylase enzymes, generated through alternative splicing, have different specific activities in Xenopus oocytes.

A single human tyrosine hydroxylase (HTH) gene has been shown previously to generate four species of mRNA by alternative splicing. The four different HTH mRNAs were independently synthesized in vitro, using the SP6 transcription system. Each of these mRNA species was able to direct the synthesis of an active form of TH following injection into Xenopus oocytes. Quantitation of synthesized HTH polypeptides allowed the determination of the relative specific activity of each individual HTH form. A significant difference in specific activity was found between each form, suggesting that alternative splicing may play a role in regulating HTH activity in vivo.

Animals↗

PubMed2005

Novel variants of human SCaMC-3, an isoform of the ATP-Mg/P(i) mitochondrial carrier, generated by alternative splicing from 3'-flanking transposable elements.

CaMCs (calcium-dependent mitochondrial carriers) represent a novel subfamily of metabolite carriers of mitochondria. The ATP-Mg/P(i) co-transporter, functionally characterized more than 20 years ago, has been identified to be a CaMC member. There are three isoforms of the ATP-Mg/P(i) carrier in mammals, SCaMC-1 (short CaMC-1), -2 and -3 (or APC-1, -3 and -2 respectively), corresponding to the genes SLC25A24, SLC25A25 and SLC25A23 respectively, as well as six N-terminal variants generated by alternative splicing for SCaMC-1 and -2 isoforms. In the present study, we describe four new variants of human SCaMC-3 generated by alternative splicing. The new mRNAs use the exon 9 3'-donor site and distinct 5'-acceptor sites from repetitive elements, in regions downstream of exon 10, the last exon in all SCaMCs. Transcripts lacking exon 10 (SCaMC-3b, -3b', -3c and -3d) code for shortened proteins lacking the last transmembrane domain of 422, 456 and 435 amino acids, and were found in human tissues and HEK-293T cells. Mitochondrial targeting of overexpressed SCaMC-3 variants is incomplete. Surprisingly, the import impairment is overcome by removing the N-terminal extension of these proteins, suggesting that the hydrophilic N-terminal domain also participates in the mitochondrial import process, as shown for the CaMC members aralar and citrin [Roesch, Hynds, Varga, Tranebjaerg and Koehler (2004) Hum. Mol. Genet. 13, 2101-2111].

3' Flanking Region↗

PubMed2002

Alternative splicing of transcripts encoding Toll-like plant resistance proteins - what's the functional relevance to innate immunity?

Innate immunity in plants and animals shares many structural and functional homologies, which suggests an ancient origin of cellular defense mechanisms in both kingdoms. Pathogen sensing in animal innate immunity is mediated by Toll-like receptors (TLRs). These receptors have TIR (Toll/interleukin-1 receptor) domains and leucine-rich repeats, which are modules also present in many plant resistance (R) proteins. Molecular analysis of transcripts encoding animal TLRs and Toll-like plant R proteins revealed many cases of alternative splicing. Recent studies of the tobacco N and the Arabidopsis RPS4 genes, both encoding Toll-like plant R proteins, showed that intron-deprived genes have reduced or no activity, suggesting that alternative splicing is a crucial component in these signaling pathways.

Alternative Splicing↗

PubMed2001

Alternative splicing of the imprinted candidate tumor suppressor gene ZAC regulates its antiproliferative and DNA binding activities.

ZAC encodes a zinc finger protein with antiproliferative activity, is maternally imprinted and is a candidate for the tumor suppressor gene on 6q24. ZAC expression is frequently lost in breast and ovary tumor-derived cell lines and down-regulated in breast primary tumors. In this report, we describe ZACDelta2, an alternatively spliced variant of ZAC lacking the sequence encoding the two N-terminal zinc fingers. Messenger RNAs encoding ZAC or ZACDelta2 were equally abundant and both proteins were nuclear. ZACDelta2 displayed an improved transactivation activity and an enhanced affinity for a ZAC binding site, suggesting that the two N-terminal zinc fingers negatively regulated ZAC binding to its target DNA sequences. Both proteins were equally efficient in preventing colony formation, indicating similar overall antiproliferative activities. However, these activities resulted from a differential regulation of apoptosis vs cell cycle progression since ZACDelta2 was more efficient at induction of cell cycle arrest than ZAC, whereas it was the reverse for apoptosis induction. Hence, these data further underline that ZAC gene is critically controlled, both at the transcriptional level through imprinting and at the functional level through alternative splicing.

Alternative Splicing↗

PubMed2002

Quantification of mouse glial cell-line derived neurotrophic factor family receptor alpha 2 alternatively spliced isoforms by real time detection PCR using SYBR Green I.

Neurturin (NTN) belongs to the glial cell-line derived neurotrophic factor (GDNF) family of growth factors. Both NTN and GDNF have been shown to potently prevent the degeneration of dopaminergic neuron in vitro and in vivo. The GDNF family receptor alpha 2 (GFR alpha-2) is the preferred receptor for NTN. In addition to the known full-length isoform (GFR alpha-2a), we have previously reported the isolation of two novel alternatively spliced isoforms (GFR alpha-2b and GFR alpha-2c). All three isoforms are expressed in all mammalian tissues examined, including human fetal brain. However, the expression levels of these isoforms have yet to be quantified. In this report, we have developed a real time polymerase chain reaction (PCR) detection method using SYBR Green I to detect the expression levels of the three splice variants (GFR alpha-2a, GFR alpha-2b and GFR alpha-2c). Of the three isoforms, GFR alpha-2a was found to be the most abundant receptor expressed in the whole murine brain. The real time PCR detection method using SYBR Green I developed in this report can be used to unambiguously quantitate expression levels of the GFR alpha-2 isoforms and can be extended to the quantitation of other alternatively spliced isoforms.

Alternative Splicing↗

PubMed2002

Expression of alternatively spliced RNA transcripts of amelogenin gene exons 8 and 9 and its end products in the rat incisor.

In addition to seven known exons of the amelogenin gene, recent studies have identified two exons downstream of amelogenin exon 7 in genomic DNA of mouse and rat. Here the spatial and temporal expression of mRNAs and of the translated proteins derived from alternative splicing of the amelogenin gene ending with exon 8 and exon 9 were examined by in situ hybridization (ISH) and immunohistochemistry (IHC). RNA signals for exons 8 and 9 were expressed in the ameloblast layer extending from early presecretory to postsecretory transitional stages of amelogenesis. IHC of amelogenin proteins that include sequences encoded by these exons demonstrated identical localization of these proteins in the ameloblast layer corresponding to RNA signals identified by ISH. There was intense immunostaining of the enamel matrix secreted by these cells. Western blotting analysis of rat enamel proteins revealed three distinct protein bands with sequences encoded by the new exons. These data confirmed the existence of the transcripts of alternatively spliced mRNAs coding for exons 8 and 9 of the amelogenin gene in rat tooth germs and suggest that the translated proteins contribute to the heterogeneity of amelogenins and have some significant roles in enamel formation and mineralization.

Alternative Splicing↗

PubMed1987

Analysis of the 5' end of the Drosophila muscle myosin heavy chain gene. Alternatively spliced transcripts initiate at a single site and intron locations are conserved compared to myosin genes of other organisms.

We have localized the transcription start site of the Drosophila melanogaster muscle myosin heavy chain (MHC) gene and find that all forms of the alternatively spliced MHC mRNA initiate at the same location. Therefore the alternative inclusion/exclusion of the 3' penultimate exon in transcripts from this gene (Bernstein, S.I., Hansen, C.J., Becker, K.D., Wassenberg, D.R., II, Roche, E.S., Donady, J.J., and Emerson, C. P., Jr. (1986) Mol. Cell. Biol. 6, 2511-2519; Rozek, C.E., and Davidson, N. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 2128-2134) does not result from the use of different 5' transcription initiation sites. This gene is the first invertebrate MHC gene shown to have TATA and CAAT box consensus sequences and a noncoding 5' exon, properties that are shared with some vertebrate and invertebrate contractile protein genes. The intron that splits the 5' noncoding region of the Drosophila MHC gene contains no major conserved elements relative to other Drosophila contractile protein genes. The introns within the coding region near the 5' end of the Drosophila MHC gene are located at the same sites as nematode and vertebrate MHC gene introns, indicating that these MHC genes are derived from a common ancestral sequence. The putative ATP binding domain encoded in the fourth exon of the Drosophila MHC gene is highly conserved relative to vertebrate, invertebrate, and non-muscle MHC genes suggesting that each of these myosins bind ATP by the same mechanism. Two divergent copies of the third exon are present within the 5' region of the Drosophila MHC gene, suggesting that alternative splicing produces MHC isoforms with different globular head regions.

Amino Acid Sequence↗

PubMed2000

Alternative splicing of gar-1, a Caenorhabditis elegans G-protein-linked acetylcholine receptor gene.

We have recently identified a gene, designated gar-1, coding for a novel form of G-protein-linked acetylcholine (ACh) receptor in Caenorhabditis elegans. Although this receptor is most closely related to muscarinic ACh receptors (mAChRs), electrophysiological analyses have shown that ligand binding specificity of the receptor is distinct from that of mAChRs. Here we report that three receptor isoforms are generated by alternative splicing of the gar-1 transcript. These receptor isoforms differ only in the third intracellular loop that is considered to be important for G protein coupling. The three splice variants, when expressed in Xenopus oocyte, displayed similar pharmacological profiles and signaling activities. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis showed that the three gar-1 mRNAs are present at all developmental stages examined. The results in this study provide evidence that alternative splicing is involved in promoting molecular diversity of G-protein-linked ACh receptors.

Alternative Splicing↗

PubMed1993

Alternatively spliced T cell receptor transcripts expressed in human T lymphocytes.

We used the anchored-polymerase chain reaction (A-PCR) procedure to study human TCR transcripts derived from a variety of polyclonal T cell populations. In this series of experiments, 31 'unusual' cDNAs, which do not include exclusively V-J-C, J-C or 5'C genomic sequences, were identified. Ten of these were found to represent distinct types of alternatively spliced TCR alpha transcripts whose structure is derived from unusual splicing of one, two or even three intervening intronic sequences. The splicing events led to either conservation of a novel exon in the mRNA structure (designated aE1 alpha-aE5 alpha) between the V-J and C segments or to deletion of the 3' V region-J segment. In three cases, the alternatively spliced exons (aE1 alpha-aE3 alpha) interrupt the open translational reading frame of the corresponding V-J alpha segment. Nineteen and two cDNA represent sterile C beta or C delta transcripts, respectively. Their structures are derived from the conservation of a non-translatable exon, aE1 beta or aE1 delta, which is precisely spliced at the 5' end of the corresponding C exon sequences. Interestingly, the 3' region of the aE1 beta sequence is homologous to the murine C beta 0 exon. Together, these results led to the characterization of nine novel exons in the TCR alpha, beta and delta loci.

Alternative Splicing↗

PubMed1996

Fibronectin mRNA alternative splicing is temporally and spatially regulated during chondrogenesis in vivo and in vitro.

Fibronectin, a component of the extracellular matrix in a variety of tissues, participates in many critical cellular processes, including differentiation, adhesion, and migration. A positive correlation exists between the presence of fibronectin and the onset of chondrogenesis, the differentiation of mesenchyme into cartilage. Heterogeneity in the structure of fibronectin is largely due to the alternative splicing of at least three exons (IIIB, IIIA, and V) during processing of a single primary transcript. We have previously shown that the fibronectin mRNA splicing patterns change during chondrogenesis (Bennett et al. [1991] J. Biol. Chem, 266:5918-5924). All of the fibronectin mRNAs from prechondrogenic chick limb mesenchyme contain exons IIIB, IIIA, and V (B + A + V +), whereas all of the fibronectin mRNAs from chick cartilage contain exons IIIB and V but do not contain exon IIIA (B + A - V +). In this study, we show that fibronectin mRNAs containing exon IIIA (FN-A) and/or the mRNAs containing exon IIIB (FN-B) are expressed in a specific and different spatiotemporal manner in the developing chick limb in vivo, as well as in limb mesenchymal cells undergoing chondrogenesis in vitro. Specifically, in situ hybridization reveals that FN-B mRNAs are present throughout the various stages (HH 20-30) of limb cartilage development in vivo, whereas FN-A mRNAs disappear following the condensation phase of chondrogenesis and absent from the resulting cartilage, Chick limb cartilage fibronectin mRNAs are therefore B + A-, as in other embryonic cartilage tissues. Furthermore, limb mesenchymal cells undergoing chondrogenesis in vitro lose FN-A mRNAs immediately following condensation, recapitulating the events that occur during chondrogenesis in vivo. These results suggest an important role for fibronectin mRNA alternative splicing during chondrogenic differentiation.

Alternative Splicing↗

PubMed2003

Calcium plays a critical role in determining the acetylcholine receptor-clustering activities of alternatively spliced isoforms of Agrin.

Neural agrin, an extracellular matrix protein secreted by motor neurons, plays a key role in clustering of nicotinic acetylcholine receptors (AChR) on postsynaptic membranes of the neuromuscular junction. The action of agrin is critically dependent on an eight-amino acid insert (z8 insert) in the third of three consecutive laminin-like globular (G3) domains near the C terminus of neural agrin. Alternatively spliced agrin isoforms in non-neural tissue including muscle lack the z8 insert and are biologically inactive. Extracellular calcium has been shown to be imperative for the AChR-clustering activity of neural agrin. It is unclear, however, whether calcium preferentially interacts with the neural isoform or whether it acts solely as an intracellular messenger that mediates agrin signaling. Here, we report the G3 domain of rat neural agrin (AgG3z8) expressed in Pichia pastoris promoted AChR clustering on surface of C2C12 myotubes in a calcium-dependent manner. Direct binding of calcium to AgG3z8 was demonstrated by trypsin digestion and thermal denaturation experiments. Moreover, calcium induced a significant change in the conformation of AgG3z8, and the effect was correlated with an enhanced binding affinity of the protein to muscle receptor. Mutation of calcium-binding residues in the G3 domain diminished the conformational change of neural agrin, reduced its binding affinity to muscle membrane, and inhibited AChR-clustering activity. Conversely, the G3 domain of muscle agrin (AgG3z0) displayed little structural change in the presence of calcium, bound poorly to muscle surface, and was inactive in AChR-clustering assays. We conclude that distinct interactions of the G3 domain with calcium determine the biological activities of alternatively spliced agrin isoforms during synapse formation.

Agrin↗

PubMed1998

Axonal injury alters alternative splicing of the retinal NR1 receptor: the preferential expression of the NR1b isoforms is crucial for retinal ganglion cell survival.

Cellular-specific splicing of the retinal NMDAR1 receptor (NR1) and expression of NMDAR2 receptor (NR2) subunits in response to optic nerve injury was investigated by in situ hybridization in adult rats. A controlled optic nerve crush led to a clear alteration in the expression of alternatively spliced NR1 variants in the retinal ganglion cell layer (GCL). The NR1-2b and NR1-4b isoforms were preferentially expressed between 2 d and 1 week after injury, whereas expression for all other isoforms remained either unchanged or decreased to barely detectable levels within 4 weeks. Cellular silver grain density for NR2 subunits also declined in the GCL after trauma. To directly test the hypothesis that NR1b expression is crucial for cell survival after axonal trauma, we administered intraocularly an antisense oligonucleotide against the NR1b isoform 2 and 3 d after injury. This led to a drastic loss of retrogradely labeled retinal ganglion cells (RGCs). Antisense targeting clearly reduced retinal NR1 protein levels, as judged by Western blot analysis, but had no effect on the cell number in control retinas. These findings point toward injury-specific changes in alternative splicing of the NR1 receptor, which are crucial for the survival of RGCs after partial axonal trauma. We therefore propose that this reflects an adaptive, rather than a pathogenic, cellular response to neurotrauma.

Alternative Splicing↗

PubMed1998

Alternative splicing events in the coding region of the cytochrome P450 aromatase gene in male rat germ cells.

Expression of cytochrome P450 mRNA in rat germ cells was characterized by reverse transcription PCR with various primers located at the 3'-end of the coding region. At least two unusual isoforms (Ex10-S and INT) of P450 aromatase (P450arom) mRNA were expressed. Analysis of their sequences demonstrated that an alternative splicing event occurred first at the exon-intron boundary of the GT consensus sequence of the last coding exon, and second in the internal 5' donor inside exon 9 used as a minor cryptic splicing site. These isoforms lacked the last coding exon which contained the heme-binding domain; in addition, for the Ex10-S transcript, the catalytic domain was also absent because of a frameshift in the open reading frame. The deduced amino acid sequences led to truncated P450arom polypeptides without the heme-binding domain, which were probably unable to convert androgens into estrogens. Adult rat germ cells are able to express P450arom mRNA, which is then translated into a biologically active enzyme which is involved in estrogen production. Moreover, for the first time, we report the existence of alternative splicing events of P45Oarom mRNA in pachytene spermatocytes and round spermatids, which probably cannot encode functional aromatase molecules.

Alternative Splicing↗