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PubMed1990

Alternative splicing of the sex determination gene transformer-2 is sex-specific in the germ line but not in the soma.

The transformer-2 (tra-2) gene of Drosophila melanogaster plays essential roles in both sexual differentiation in the female soma and spermatogenesis in the male germ line. In the female soma, tra-2 is known to act with other genes in the sex determination regulatory cascade to control the sex-specific alternative splicing of transcripts from the doublesex gene. Here, we determine whether or not any sex-specific tra-2 products are expressed that may account for either of these sex-specific activities. Sequence analysis of the tra-2 gene and 10 tra-2 cDNA clones coupled with nuclease protection analysis reveals a variety of alternatively spliced tra-2 mRNAs that each encode one of four distinct but overlapping polypeptides. Three of the encoded polypeptides contain both a ribonucleoprotein consensus sequence and arginine/serine-rich regions, suggesting a direct role for these products in RNA splicing. We show that although two transcripts are expressed male specifically in the germ line, the tra-2 transcripts expressed in the soma are not sex-specific. The translation of products from a tra-2-lacZ fusion gene in both sexes suggests that the female-specific functioning of tra-2 in somatic tissues is not attributable to a translational mechanism. We suggest that tra-2 activity in somatic tissues is regulated through a post-translational sex-specific interaction with the product of the tra gene rather than through the expression of a female-specific tra-2 polypeptide.

Amino Acid Sequence↗

PubMed1998

Autoregulation of transformer-2 alternative splicing is necessary for normal male fertility in Drosophila.

In the male germline of Drosophila the transformer-2 protein is required for differential splicing of pre-mRNAs from the exuperantia and att genes and autoregulates alternative splicing of its own pre-mRNA. Autoregulation of TRA-2 splicing results in production of two mRNAs that differ by the splicing/retention of the M1 intron and encode functionally distinct protein isoforms. Splicing of the intron produces an mRNA encoding TRA-2(226), which is necessary and sufficient for both male fertility and regulation of downstream target RNAs. When the intron is retained, an mRNA is produced encoding TRA-2(179), a protein with no known function. We have previously shown that repression of M1 splicing is dependent on TRA-2(226), suggesting that this protein quantitatively limits its own expression through a negative feedback mechanism at the level of splicing. Here we examine this idea, by testing the effect that variations in the level of tra-2 expression have on the splicing of M1 and on male fertility. Consistent with our hypothesis, we observe that as tra-2 gene dosage is increased, smaller proportions of TRA-2(226) mRNA are produced, limiting expression of this isoform. Feedback regulation is critical for male fertility, since it is significantly decreased by a transgene in which repression of M1 splicing cannot occur and TRA-2(226) mRNA is constitutively produced. The effect of this transgene becomes more severe as its dosage is increased, indicating that fertility is sensitive to an excess of TRA-2(226). Our results suggest that autoregulation of TRA-2(226) expression in male germ cells is necessary for normal spermatogenesis.

Alternative Splicing↗

PubMed1992

Genomic structure and alternative splicing of 519, a gene expressed late after T cell activation.

Relatively little is known about the transcriptional control of genes expressed late after T cell activation. We have identified four genes expressed 3 to 5 days after T cell activation by alloantigen or mitogen. Here we report the genomic organization of 519, one of these late T cell activation Ag. Analysis of the genomic clone revealed that 519 consists of six exons. Ribonuclease protection experiments indicated that the most abundant transcript arising from this region is an alternatively spliced form of 519, referred to as 520, which lacks exon 2 and is similar in sequence to NKG5, a cDNA identified in NK cells. These experiments also revealed the existence of two other alternatively spliced RNA transcripts, with heterogeneity in exon 2. Primer extension analysis and ribonuclease protection assays demonstrated that there are two prominent start sites for transcription; however, there is no evidence for the NKG5 transcript in T cells, indicating that NKG5 may represent a NK cell-specific form of 520. The 5' flanking region of this gene contains several previously identified sequences involved in transcriptional regulation, as well as some potentially interesting novel conserved motifs.

Antigens, Differentiation, T-Lymphocyte↗

PubMed1991

Alternative splicing generates two variants of the alpha 1 subunit of the inhibitory glycine receptor.

The inhibitory glycine receptor (GlyR) in mammalian spinal cord displays pharmacological and molecular heterogeneity of its strychnine binding alpha subunit. Here, cDNAs were isolated which encode a variant (alpha ins 1) of the rat GlyR alpha 1 subunit that contains eight additional amino acids in its putative cytoplasmic domain. Analysis of the corresponding genomic sequence showed that alpha ins 1 transcripts result from alternative splice acceptor site selection. S1 nuclease protection experiments, Northern blot analysis, and RNA amplification by polymerase chain reaction revealed alpha 1 and alpha ins 1 mRNA in postnatal spinal cord, but not in other brain regions. Expression of synthetic alpha ins 1 RNA in Xenopus oocytes generated glycine-gated strychnine-sensitive chloride channels. These data indicate that alternative splicing contributes to GlyR alpha subunit heterogeneity in the mammalian central nervous system.

Amino Acid Sequence↗

PubMed1994

Alternative splicing of the NF2 gene and its mutation analysis of breast and colorectal cancers.

To investigate a potential role of NF2, the gene responsible for hereditary bilateral acoustic neurinomas, during carcinogenesis of non-neurogenic tissues, we screened somatic mutations of NF2 in 55 breast cancers and 44 colorectal carcinomas by an RNase protection assay coupled with the reverse-transcriptase polymerase chain reaction (RT-PCR). By screening the entire coding region of the gene in these tumors, we detected missense mutations in the exon encoding the alpha-helical domain of the NF2 product in two colorectal carcinomas. No mutations were detected in any of the breast cancers. Our results suggested that inactivation of the NF2 gene was associated with carcinogenesis in some, but not the majority of, colorectal tumors. In the course of these analyses, we found various alternatively-spliced forms of NF2 transcript. These variants showed no specificity among the tissues examined except for one that resulted from alternative splicing at the 3'-region; this form was more abundantly expressed in skeletal and cardiac muscles than in other tissues.

Amino Acid Sequence↗

PubMed1993

Expression of alternatively-spliced glutamate receptors in human hippocampus.

Rat glutamate receptors have been shown to be expressed as two developmentally regulated, alternatively spliced isoforms. We have investigated the expression of these isoforms of GluRA and GluRB in the human hippocampus. The expression pattern of the mRNAs coding for these subunits does not correspond to that in the rat hippocampus, both isoforms being preferentially expressed in the dentate gyrus and CA1 regions, with lower expression in CA3, with the exception of GluRB flop, where hybridization in CA3 is only lower than in dentate gyrus. Cloning of cDNA from human frontal cortex has also revealed that the two isoforms of human GluRB have virtual nucleotide sequence identity with the alternative exons in the rat, confirming the usefulness of oligonucleotides complementary to the rat cDNAs as probes for these receptor subunits in human neuropsychiatric disorders.

Alternative Splicing↗

PubMed1990

Activated T cells transcribe an alternatively spliced mRNA encoding a soluble form of Qa-2 antigen.

Among the best characterized non-classical mouse major histocompatibility antigens are the Qa-2 molecules. These proteins can serve as targets for allogenic cytotoxic T cells and as signal transducing molecules. They are structurally similar to H-2 transplantation antigens in their N-terminal and beta 2-microglobulin binding domains but differ at their C-termini. While the H-2 antigens span the cell membrane, the Qa-2 molecules are attached to the cell surface via phospholipid anchors. The genetic information encoding this attachment is contained in exon 5. In concanavalin A activated splenocytes the expression of membrane bound Qa-2 antigens declines and, simultaneously, soluble forms of Qa-2 molecules are secreted. We demonstrate here that the soluble Qa-2 polypeptides are translated from alternatively spliced mRNAs lacking exon 5, while the membrane forms are encoded by the full-size transcripts. In cultured cells the alternative splicing of the Qa-2 message is induced by T-cell activation splicing of the Qa-2 message is induced by T-cell activation with concanavalin A. The canonical mRNA encoding the membrane form of Qa-2 predominates in unstimulated mouse tissues but the cultured cell lines, like activated T cells, express enhanced levels of the truncated mRNA. In some cell lines almost all Qa-2 transcripts lack exon 5. For example, in L cells, mRNAs encoding soluble Qa-2 molecules are at least 10 times more abundant than Qa-2 transcripts encoding phospholipid anchored antigens. These findings are discussed in terms of potential functions of membrane bound and secreted Qa-2 molecules.

Amino Acid Sequence↗

PubMed1985

Alternative splicing accounts for the four forms of myelin basic protein.

We have isolated cDNA clones encoding the four different forms of mouse myelin basic protein (MBP) and have analyzed the structure of the MBP gene. The three larger forms of MBP differ from the smallest by the inclusion of either or both of two short amino acid sequences at positions 57 and 124 of the smallest protein. The mouse genome contains a single MBP gene comprised of seven exons. The two amino acid sequences present only in the larger MBPs are encoded by separate exons. Furthermore, all exons in the coding region begin or end in complete codons so that alternative splicing does not alter the reading frame. We conclude that the four forms of this myelin protein are encoded in separate mRNAs, each derived by a simple alternative splicing of the primary MBP gene transcript. Comparison of the amino acid sequence encoded by each exon with a recent model of the secondary structure of MBP suggests that each of the seven exons encodes one or two of the predicted structural motifs of the protein.

Amino Acid Sequence↗

PubMed1991

Developmentally regulated alternative splicing in the Xenopus laevis c-Myc gene creates an intron-1 containing c-Myc RNA present only in post-midblastula embryos.

Two distinct c-Myc RNA classes have been identified in Xenopus laevis, presumably expressed from the duplicated c-Myc locus (1, 6). The major Xenopus c-Myc transcripts arise from sites termed P1 and P2 similarly to those of the mammalian c-Myc genes. I have used a cloned Xenopus c-Myc gene to examine the regulated pattern of expression from this gene during early Xenopus embryogenesis. Analysis of the pattern of transcript processing indicates that not only are P1 and P2 differentially active during early development but alternatively spliced c-Myc RNAs are generated which contain sequences of the first intron. These intron-1 containing c-Myc RNAs are generated by alternative splicing of transcripts initiated from the major transcription start site, P2, and are observed only in RNA samples from post-midblastula embryos or Xenopus tissue culture cells. Xenopus tissue culture cells synthesize two major c-Myc proteins (p61 and p64). Xenopus RNAs that do not contain intron-1 sequences synthesize only the p61 species. Two closely spaced ATG codons at the 5' end of exon-2 are utilized equivalently to generate a p61 doublet. Intron-1 containing RNAs utilize an ATG codon in the intron sequences to synthesize the p64 species as well as the exon-2 ATG codons to synthesize the p61 doublet.

Animals↗

PubMed1987

Alpha-tropomyosin gene organization. Alternative splicing of duplicated isotype-specific exons accounts for the production of smooth and striated muscle isoforms.

We have previously isolated and characterized cloned complementary DNAs (cDNAs) for striated and smooth muscle alpha-tropomyosin. The sequences of these cDNA clones suggested that these two isoforms were encoded by the same gene. Here, we have determined the complete structure of the alpha-tropomyosin (alpha-TM) gene, establishing that a single gene, with a sequence complexity of 28 kilobase pairs, is split into 12 exons and produces the smooth and striated muscle alpha-TM mRNA isoforms by alternative splicing of a minimum of five exchangeable isotype-specific exons. The elucidation of the intron/exon organization of alpha-TM suggests that this gene evolved from an ancestral gene encoding a 21-aa protein that might represent the primordial actin binding domain. Sequence comparison between the pairs of exons coding for the "isotype switch regions" and among the corresponding regions of tropomyosin genes in a variety of species ranging from insects to mammals, suggests that the alternatively spliced exons are very old and might have arisen before the radiation of the arthropods, more than 600 million years ago. Additionally, the examination of the intronic sequences has uncovered potential alternative intramolecular secondary structures (hairpin-loop structures) which might be involved in the tissue-specific expression of the duplicated and mutually exclusive alpha-TM isotype-specific exons.

Animals↗

PubMed1995

Identification of a novel alternatively spliced agrin mRNA that is preferentially expressed in non-neuronal cells.

A novel agrin isoform was identified based on the isolation of an agrin cDNA from E9 chick brain that lacked 21 base pairs (bp) in the NH2-terminal encoding region of the agrin mRNA. Reverse transcription-polymerase chain reaction (RT-PCR) of E9 chick brain mRNA confirmed the existence of this agrin isoform in brain, although the novel splice variant represents a minor fraction of agrin mRNA in brain. However, upon analysis of chick brain astrocyte mRNA, smooth muscle mRNA, and cardiac muscle mRNA by RT-PCR, we show that this novel agrin isoform is the predominant agrin isoform in these non-neuronal cell populations. We extended our analyses to examine the expression of this agrin mRNA isoform during chick development and show that the agrin mRNA lacking this 21-bp exon is up-regulated with brain development, consistent with the increase in glial number during brain development, while the agrin isoform that does not undergo splicing and thus contains the 21-bp exon is down-regulated in brain development. Because the 21-bp exon is inserted in the region of chick agrin which encodes the putative signal sequence of agrin, with the signal peptidase site immediately preceding the putative first amino acid of the mature protein being deleted as a result of splicing, these data raise the interesting possibility that the presence or absence of this alternatively spliced exon may differentially regulate processing of the agrin protein in neuronal and non-neuronal cells, respectively.

Agrin↗

PubMed1991

Human alpha 3(VI) collagen gene. Characterization of exons coding for the amino-terminal globular domain and alternative splicing in normal and tumor cells.

We recently reported the isolation and sequencing of human cDNA clones corresponding to the alpha 3 chain of type VI collagen (Chu, M.-L., Zhang, R.-Z., Pan, T.-c., Stokes, D., Conway, D., Kuo, H.-J., Glanville, R., Mayer, U., Mann, K., Deutzmann, R., and Timpl, R. (1990) EMBO J. 9, 385-393). The study indicates that the amino-terminal globular domain of the alpha 3(VI) chain consists of nine repetitive subdomains of approximately 200 amino acid residues (N1-N9) and the gene appeared to undergo alternative splicing since some clones lacked regions encoding the N9 and part of the N3 subdomains. In the present study, we report the exon structure for the region encoding the amino-terminal globular domain of the human alpha 3(VI) chain. The nine repetitive subdomains are encoded by 10 exons spanning 26 kilobase pairs of genomic DNA. Eight of the repetitive subdomains (N2-N9) were found to be encoded by separate exons of approximately 600 base pairs each. The only exception is the N1 subdomain which is encoded by two exons of 417 and 146 base pairs. Characterization of the exon/intron structure showed that the cDNA variants were the result of splicing out of exon 9 (encoding the N9 subdomain) and part of exon 3 (encoding the N3 subdomain). Nuclease S1 analysis and the polymerase chain reaction demonstrated that exon 7 (N7 subdomain) was also subject to alternative splicing in normal skin fibroblasts. Examination of these splicing events by nuclease S1 analysis in normal fibroblasts, three different human tumor cell lines, and several human tissues showed that splicing out of exon 9 is much more efficient in normal as compared to tumor cells.

Adult↗

PubMed2003

The alternatively spliced deltae13 transcript of the rabbit calcitonin receptor dimerizes with the C1a isoform and inhibits its surface expression.

Numerous alternatively spliced transcripts are generated from the gene for the G protein-coupled calcitonin receptor, and some of the splice variants show differences in receptor-mediated signaling events. This study showed that the deltae13 splice variant of the rabbit calcitonin receptor is expressed together with the more common C1a in osteoclast-like cells. Since other G protein-coupled receptors form homo- or heterodimers, we examined whether heterodimerization of the calcitonin receptor splice variants occurs and, if so, whether it affects the function of the receptor. Homodimers of both isoforms and deltae13/C1a heterodimers were detected by co-immunoprecipitation and fluorescence resonance energy transfer analysis. In contrast to the C1a isoform, the deltae13 isoform was not efficiently transported to the cell surface. When co-expressed with the C1a splice variant, the deltae13 isoform colocalized with the C1a isoform within the cell but not at the cell surface. Furthermore, the overexpression of the deltae13 variant led to a significant reduction of the C1a surface expression and consequently a reduction of the cAMP response and Erk phosphorylation after ligand stimulation. We therefore suggest that the deltae13 variant of the rabbit calcitonin receptor acts to regulate the surface expression of the C1a isoform.

Alternative Splicing↗

PubMed2005

Human cyclo-oxygenase-1 and an alternative splice variant: contrasts in expression of mRNA, protein and catalytic activities.

The two COX (cyclo-oxygenase) isoenzymes COX-1 and -2 catalyse the initial step in the conversion of arachidonic acid into PG (prostaglandin) hormones. The identification of an mRNA transcript encoding a splice variant of human COX-1 was reported more than a decade ago [Diaz, Reginato and Jimenez (1992) J. Biol. Chem. 267, 10816-10822], yet catalytic activity and tissue expression of the corresponding spliced protein remained uncharacterized. The splice variant lacks amino acids 396-432, corresponding to the last 37 amino acids of exon 9 of the gene encoding COX-1. These amino acids form a loop at one side of the peroxidase active site of the protein. We expressed the full-length and spliced COX-1 cDNAs in COS-7 and Sf9 insect cells, and determined the PG-forming activity using incubations with radiolabelled arachidonic acid and HPLC analyses. When expressed in either system, abundant PG formation was observed with the full-length COX-1, whereas the spliced protein did not form any detectable product. Peroxidase activity was readily detected in microsomes prepared from COS-7 cells transfected with COX-1 but not with the splice variant. In reverse transcriptase-PCR experiments, we detected the mRNA for the alternatively spliced and full-length COX-1 in human brain, tonsil and colon tissue, yet we were unable to detect expression of the spliced protein in the same tissues using immunoprecipitation and Western-blot analyses. We conclude that, whereas the mRNA transcript for the spliced COX-1 is present in various human tissues, the corresponding protein is either not formed or subject to rapid proteolytic degradation.

Alternative Splicing↗

PubMed2006

Comparative studies on Ureide Permeases in Arabidopsis thaliana and analysis of two alternative splice variants of AtUPS5.

The recovery of free purine and pyrimidine bases and their degradation products represent alternative pathways in plant cells either to synthesize nucleotides (salvage pathways) by low energy consumption or to reuse organic nitrogen. Such recycling of metabolites often requires their uptake into the cell by specialized transport systems residing in the plasma membrane. In plants, it has been suggested that several protein families are involved in this process, but only a few transporters have so far been characterized. In this work, gene expression, substrate specificities, and transport mechanisms of members of the Ureide Permease family in Arabidopsis (AtUPS) were analyzed and compared. Promoter-GUS studies indicated that the members of the family have distinct and partially overlapping expression patterns with regard to developmental stages or tissue specific localization. In addition, two alternative splice variants of AtUPS5, a novel member of the transporter family, were identified and investigated. The abundance of both alternative mRNAs varied in different organs, while the relative amounts were comparable. AtUPS5l (longer isoform) shares similar structural prediction with AtUPS1 and AtUPS2. In contrast, AtUPS5s (shorter isoform) lacks two transmembrane domains as structural consequence of the additional splice event. When expressed in yeast, AtUPS5l mediates cellular import of cyclic purine degradation products and pyrimidines similarly to AtUPS1 and AtUPS2, but differences in transport efficiencies were observed. AtUPS5s, however, could not be shown to mediate uptake of these compounds into yeast cells and might therefore be defective or have a different function.

Alternative Splicing↗

PubMed1997

Unique gene organization: alternative splicing in Drosophila produces two structurally unrelated proteins.

The Ub80 gene in eukaryotes produces a ubiquitin fusion protein in which ubiquitin is fused in frame to a tail protein (Redman and Rechsteiner, 1988; Finley et al., 1989; Barrio et al., 1994). The tail protein is incorporated into the ribosome, and ubiquitin is thought to act as a chaperone. The DUb80 gene of Drosophila melanogaster was cloned by Barrio et al. (1994) and contains a 5'-untranslated exon, followed by a large intron and then the first coding exon. We report that the large intron of DUb80 contains an open reading frame, which produces a 259-aa protein (IP259) that is conserved in eukaryotes from yeast to mammals. Transcription of the DUb80 and IP259 mRNAs begins at the same start sites. However, alternate splicing of the primary transcript produces two structurally unrelated proteins. This is the second reported instance of two structurally unrelated proteins being produced via alternate splicing, suggesting that this form of genomic organization may be more common than previously thought.

Amino Acid Sequence↗

PubMed2025

CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing.

Pre-mRNA splicing is kinetically coupled to transcription as shown by the widespread effects of transcription speed on alternative splicing (AS) outcomes. The molecular basis for such kinetic coupling is incompletely understood, but one potential mechanism is through elongation rate-dependent alternative folding pathways of the nascent pre-messenger RNA (pre-mRNA). To search for RNA structures in nascent pre-mRNA, we modified Sequencing of Psoralen Crosslinked, Ligated And Selected Hybrids (SPLASH) [J. G. Ashley Aw et al., Mol. Cell 62, 603-617 (2016)] for use with Chromatin Associated RNA. We applied this method called Chromatin Associated RNA (CAR)-SPLASH to cells expressing wild-type and slow mutant RNA polymerase II and identified >3,000 intramolecular RNA duplexes of which >400 are proximal to splice sites. Antisense oligonucleotide (ASO) disruption of several such duplexes that sequester splice sites has a major impact on AS outcomes, even though the ASOs do not directly disrupt splice sites. ASO disruption of these regulatory elements that we designate "RNA kinetic switches" modified AS of NISCH Exon 18, GAK Exon 7, and MEGF8 Exon 14 in a way that depends on the rate of transcription elongation. We propose that these switches mediate kinetic coupling via the effects of transcription speed on folding of nascent RNA structures that modulate AS and that many nascent RNA structures can thereby serve as targets for splice-modifying ASOs.

RNA Precursors↗

PubMed2001

Alternative splicing of transcripts expressed by the Manduca sexta allatotropin (Mas-AT) gene is regulated in a tissue-specific manner.

The Manduca allatotropin (Mas-AT) gene is expressed as at least three mRNA isoforms that differ from each other by alternative splicing. The location at which the alternative exons are included in the mature mRNAs occur within the open reading frame, so that three different propeptides are predicted as translation products. In the pharate adult insect, the major mRNA isoform expressed in the brain and frontal ganglion differs from that expressed in the nerve cord. Examination of the deduced translations of the alternative exons reveals the presence of three additional Mas-AT-like sequences that are flanked by basic amino acid residues. Therefore, the Mas-AT-like sequences present within the gene may be derived from a duplication of an ancestral Mas-AT-like sequence followed by divergence.

Alternative Splicing↗