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PubMed1997

Four 5-hydroxytryptamine7 (5-HT7) receptor isoforms in human and rat produced by alternative splicing: species differences due to altered intron-exon organization.

The serotonin (5-HT) 5-HT7 receptor subtype is thought to mediate a number of physiological effects in mammalian brain and periphery. Previous studies suggested that alternative splicing might contribute to 5-HT7 receptor diversity as well. We now report that alternative splicing in human and rat tissues produces four 5-HT7 receptor isoforms that differ in their predicted C-terminal intracellular tails. Human and rat partial 5-HT7 cDNAs and intronic sequences were identified and compared. In rat tissues, three 5-HT7 isoforms, here called 5-HT7(a), 5-HT7(b), and 5-HT7(c), are found. Rat 5-HT7(a) [448-amino acid (aa)] and 5-HT7(b) (435-aa) forms arise from alternative splice donor sites. A third new isoform found in rat, 5-HT7(c) (470-aa), results from a retained exon cassette. Three 5-HT7 mRNA isoforms were also identified in human tissues, where only one isoform was previously described. Two human isoforms represent 5-HT7(a) and 5-HT7(b) forms (445- and 432-aa), but the third form does not correspond to 5-HT7(c). Instead, it constitutes a distinct isoform, 5-HT7(d) (479-aa), resulting from retention of a separate exon cassette. 5-HT7(d) transcripts are not present in rat because the 5-HT7(d)-specifying exon is absent from the rat 5-HT7 gene. A frame-shifting homologue of the rat 5-HT7(c)-Specifying exon is present in the human gene but is not used in the human tissues examined. Tissue-specific splicing differences are present in human between brain and spleen. These studies suggest that alternative splicing may contribute to diversity of 5-HT7 receptor action and that the human and rat repertoires of 5-HT7 splice variants are substantially different.

Alternative Splicing↗
PubMed1987

Multiple sites of alternative splicing of the rat fibronectin gene transcript.

We describe analyses of the structure and expression of the rat fibronectin gene with particular attention to the 40-kb stretch from the center of the gene which encodes 17 type-III repeating units. Each repeat is precisely separated from its neighbors by introns and most are encoded by pairs of exons. Three repeats are encoded precisely by single exons and two of these (EIIIA and EIIIB) are alternatively spliced in a cell type-specific fashion. A third site of alternative splicing (EIIIB) reported here is similar in expression to the previously described EIIIA segment. Both are excluded from mRNA in liver cells and are, therefore, absent from plasma fibronectin. These two alternative splices, plus a third one (V) reported previously, can occur in all possible combinations giving 12 fibronectin mRNAs from a single gene. These splicing variations account for most but not all of the known fibronectin subunit variants. We report investigations designed to detect other regions of alternative splicing. We also show that the pattern of alternative splicing is somewhat altered on oncogenic transformation.

Amino Acid Sequence↗
PubMed2004

Human gastric tissues simultaneously express the classical and alternative splicing cholecystokinin-B/gastrin receptors.

To explore whether cholecystokinin-B/gastrin receptor (CCKBRwt) gene and its alternative splicing variant preserving intron 4 (CCKBRi4sv) are expressed in human gastric carcinoma cell line and tissue, we detect mRNA expression of CCKBRwt and CCKBRi4sv in 30 gastric carcinoma and their corresponding normal tissues, 10 gastritis, and 2 autopsied normal stomach specimens as well as in a gastric carcinoma cell line SGC-7901 cells by RT-PCR and sequencing. The results revealed that human normal, inflammatory, and malignant gastric tissues simultaneously expressed the classical and alternative splicing cholecystokinin-B/gastrin receptor genes. The alternative splicing variant contains the intron 4 of cholecystokinin-B/gastrin receptor gene.

Alternative Splicing↗
PubMed1995

Genomic organization of the human alpha-adducin gene and its alternately spliced isoforms.

The cDNA for the human alpha-adducin gene has been cloned, and different alternately spliced forms have been identified. We report the complete genomic organization of the human alpha-adducin gene and these alternately spliced forms. The human alpha-adducin gene, spanning approximately 85 kb, consists of 16 exons ranging in size from 34 to 1892 bp. One of the spliced forms of the human alpha-adducin gene results from alternate use of the 5' splice donor site for exon 10, while another results in a truncated protein following insertion of 34 bp comprising exon 15, followed by a premature stop codon. This alternate spliced form of alpha-adducin is predicted to result in an altered carboxyl terminus that would eliminate a protein kinase and calmodulin binding site. Seven nucleotide substitutions and 4 insertion/deletions were also identified. The 5' region of the human alpha-adducin gene contains one Sp1 site, two AP2 sites, and two CAAT boxes. No TATA box was apparent, consistent with features of a housekeeping gene. We have mapped another cDNA within the first intron of the human alpha-adducin gene, suggesting overlapping genes in this 4p16.3 genomic region.

Alternative Splicing↗
PubMed2005

Alternative splicing of MDM2 mRNA in lung carcinomas and lung cell lines.

The MDM2 gene is overexpressed in several human tumors and its product may be processed into various isoforms. Recently, alternative splicing forms of MDM2 mRNA have been detected in various types of tumors. In this study, lung tissue from human non small cell lung cancers was examined for MDM2 mRNA splicing variants by nested RT-PCR. Of the 117 lung cancer tissue samples analyzed, a total of 31 (26.5%) had splice variants for the MDM2 gene, while 59 (50.4%) had undetectable levels of MDM2 transcript. Further analysis indicated that the predominant variant for 26 of the 31 samples with alternative MDM2 splicing products was MDM2-657, a splice variant lacking exons 3-11. Significant associations were found between the frequency of alternative splicing and the gender and smoking habits of the patients. Approximately 36% of male patients had alternative splicing of MDM2 compared with only 9.5% of female patients (P = 0.008); 44.2% of the smoker patients had alternative MDM2 splice forms versus 16.2% of nonsmokers (P = 0.003). Furthermore, most normal lung cell lines examined possessed only full-length MDM2 mRNA, while among several lung cancer cell lines, only H1355 and CaLu-1 cells lacked alternatively spliced MDM2 transcripts. When H1355 cells were treated in vitro with the cigarette smoke carcinogen benzo[a]pyrene (B[a]P) or the B[a]P metabolite benzo[a]pyrene diolepoxide (BPDE), three MDM2 splicing products were detected by nested RT-PCR. Finally, with the use of several specific inhibitors, we found that BPDE-induced MDM2 mRNA alternative splicing in H1355 cells may occur through the PI3K or MAPK pathway. Overall, our results suggest that carcinogens present in cigarette smoke increase the risk of alternative MDM2 splicing, which is highly associated with lung cancer.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed2006

Allergy-driven alternative splicing of IL-13 receptor alpha2 yields distinct membrane and soluble forms.

IL-13 is a key mediator of allergic inflammation. Its diverse functions are mediated by a complex receptor system including IL-4Ralpha, IL-13Ralpha1, and IL-13Ralpha2. IL-4Ralpha and IL-13Ralpha1 form a high-affinity signaling heterodimer. IL-13Ralpha2 binds IL-13 with high affinity and has been found to exist in membrane and soluble forms. Soluble IL-13Ralpha2 has been postulated as a critical endogenous modulator of IL-13 responses. However, the mechanism of generation for the soluble form remains unclear. We present the initial study that a mechanism for generation of the soluble form is alternative splicing and that alternative splicing yields a distinct form of soluble IL-13Ralpha2. We found that several mouse organs expressed two IL-13Ralpha2 transcripts, the 1152-bp transcript encoding the full-length protein and the 1020-bp transcript lacking exon10, which encodes the transmembrane region. Deletion of exon 10 (DeltaEx10) caused a frameshift resulting in a different amino acid sequence from position 327 to position 339 and early termination. Constructs encoding both splice variants were transfected into WEHI-274.1 cells. Transfectants expressing the full-length transcript had IL-13Ralpha2 on the cell surface but produced minimal soluble IL-13Ralpha2 in the supernatants. In contrast, transfectants expressing the DeltaEx10 transcript displayed no membrane IL-13Ralpha2 but secreted high levels of soluble IL-13Ralpha2 capable of inhibiting IL-13 signaling. Both variants bound IL-13, but the DeltaEx10 variant displayed approximately 2-fold increase in IL-13 binding activity. Expression of the two IL-13Ralpha2 transcripts was differentially regulated in vivo in an experimental allergic asthma model. Thus, alternatively spliced variants of IL-13Ralpha2 may have a distinct biologic function in vivo.

Alternative Splicing↗
PubMed1996

Alternative splicing of human inducible nitric-oxide synthase mRNA. tissue-specific regulation and induction by cytokines.

Human inducible nitric-oxide synthase (iNOS) is responsible for nitric oxide synthesis in response to inflammatory mediators. The human iNOS gene, containing 26 exons, encodes a protein of 131 kDa. This study was aimed at investigating the presence of alternative splicing of human iNOS mRNA. Total RNA from human alveolar macrophages, nasal and bronchial epithelial cells, and several human tissues was transcribed to cDNA and analyzed using polymerase chain reaction with specific primers for segmental analysis of the iNOS gene. Four sites of alternative splicing were identified by sequence analysis; these included deletion of: (i) exon 5; (ii) exons 8 and 9; (iii) exons 9, 10, and 11; and (iv) exons 15 and 16. The deduced amino acid sequences of the novel iNOS cDNAs predict one truncated protein (resulting from exon 5 deletion) and three iNOS proteins with in-frame deletions. Southern analyses of polymerase chain reaction products were consistent with tissue-specific regulation of alternative splicing. In cultured cells, iNOS induction by cytokines and lipopolysaccharide was associated with an increase in alternatively spliced mRNA transcripts. Because iNOS is active as a dimer, the novel forms of alternatively spliced iNOS may be involved in regulation of nitric oxide synthesis.

Alternative Splicing↗
PubMed2002

Protein-based analysis of alternative splicing in the human genome.

Understanding the functional significance of alternative splicing and other mechanisms that generate RNA transcript diversity is an important challenge facing modern-day molecular biology. Using homology-based, protein sequence analysis methods, it should be possible to investigate how transcript diversity impacts protein structure and function. To test this, a data mining technique ("DiffHit") was developed to identify and catalog genes producing protein isoforms which exhibit distinct profiles of conserved protein motifs. We found that out of a test set of over 1,300 alternatively spliced genes with solved genomic structure, over 30% exhibited a differential profile of conserved InterPro and/or Blocks protein motifs across distinct isoforms. These results suggest that motif databases such as Blocks and InterPro are potentially useful tools for investigating how alternative transcript structure affects gene function.

Algorithms↗
PubMed2006

Inferring global levels of alternative splicing isoforms using a generative model of microarray data.

MOTIVATION: Alternative splicing (AS) is a frequent step in metozoan gene expression whereby the exons of genes are spliced in different combinations to generate multiple isoforms of mature mRNA. AS functions to enrich an organism's proteomic complexity and regulates gene expression. Despite its importance, the mechanisms underlying AS and its regulation are not well understood, especially in the context of global gene expression patterns. We present here an algorithm referred to as the Generative model for the Alternative Splicing Array Platform (GenASAP) that can predict the levels of AS for thousands of exon skipping events using data generated from custom microarrays. GenASAP uses Bayesian learning in an unsupervised probability model to accurately predict AS levels from the microarray data. GenASAP is capable of learning the hybridization profiles of microarray data, while modeling noise processes and missing or aberrant data. GenASAP has been successfully applied to the global discovery and analysis of AS in mammalian cells and tissues. RESULTS: GenASAP was applied to data obtained from a custom microarray designed for the monitoring of 3126 AS events in mouse cells and tissues. The microarray design included probes specific for exon body and junction sequences formed by the splicing of exons. Our results show that GenASAP provides accurate predictions for over one-third of the total events, as verified by independent RT-PCR assays. SUPPLEMENTARY INFORMATION: http://www.psi.toronto.edu/GenASAP.

Algorithms↗
PubMed1997

Six novel transcripts that remove a huge intron ranging from 250 to 800 kb are produced by alternative splicing of the 5' region of the dystrophin gene in human skeletal muscle.

The dystrophin gene, which is mutated in patients with Duchenne and Becker muscular dystrophies, comprises 79 exons and is thus the largest known human gene. A full spectrum of splicing of dystrophin transcript has not been elucidated yet. In this study, 6 novel alternative splicing reactions were discovered in the 5' region by amplifying the cDNA corresponding to exons M1 through 18. Two of these novel transcripts maintain the translational reading frame and are presumed to produce truncated dystrophin, while the other four have disrupted reading frames. The physical distance between splice donor and acceptor sites ranged from 250 kb to 800 kb. Furthermore, the same six alternative splicing products were obtained from mouse skeletal muscle cDNA. This indicated that these novel alternative splicing events are conserved in humans and mice.

Alternative Splicing↗
PubMed1990

Gene expression from the c-erbA alpha/Rev-ErbA alpha genomic locus. Potential regulation of alternative splicing by opposite strand transcription.

Alternative splicing of the c-erbA alpha gene transcript generates mRNAs encoding a thyroid hormone (T3) receptor (alpha 1) and a non-T3-binding variant (alpha 2). Also encoded at this genomic locus is Rev-ErbA alpha (Rev), a non-T3-binding member of the T3/steroid hormone receptor family. The DNA strand coding for Rev is opposite of that encoding the c-erbA alpha proteins, such that bidirectional transcription is required to generate the Rev and alpha 2 mRNAs. We have used cycloheximide as a tool for studying the regulation of gene expression from this complex genomic locus. In 235-1 cells cycloheximide treatment increased Rev mRNA levels by 50-100-fold. The effect was detectable after a 1-2-h incubation with 20 micrograms/ml cycloheximide and maximal at 24 h. The cycloheximide-induced increase in Rev gene expression was due to inhibition of protein synthesis since anisomycin caused a similar induction of Rev mRNA. Nuclear run-on assays revealed an approximately 10-fold increase in the transcriptional rate of the Rev gene during cycloheximide treatment. In addition, cycloheximide stabilized the Rev mRNA, as evidenced by half-life determinations in the presence of actinomycin D (5 ng/ml). Thus, labile proteins repress basal Rev gene expression both transcriptionally and post-transcriptionally. Cycloheximide treatment also increased alpha 1 and decreased alpha 2 mRNA levels, with the alpha 1/alpha 2 ratio increasing approximately 10-fold. Interestingly, however, these effects appeared not to be due to changes in rates of transcription or degradation of either mRNA. A likely alternative, given the structure of the c-erbA alpha gene, is that inhibition of protein synthesis resulted in a change in the c-erbA alpha splicing pattern. We hypothesize that this may be causally related to the accumulation of Rev mRNA (or the nascent Rev gene transcript), which could inhibit splicing to alpha 2 by hybridizing to complementary sequences, favoring alpha 1 mRNA production. Since alpha 1 is a T3 receptor whereas alpha 2 is an inhibitor of T3 action, such changes could influence target cell responsiveness to T3.

Cell Line↗
PubMed1997

Alternative splicing of the unique "PLUS" domain of chicken PG-M/versican is developmentally regulated.

We investigated the occurrence of alternatively spliced forms (V0, V1, V2, and V3) of PG-M/versican, a large chondroitin sulfate proteoglycan in developing chicken retinas, using the reverse transcription-polymerase chain reaction. We characterized the PLUS domain, which is apparently unique to the chicken molecule and is regulated by alternative splicing. PG-M in chicken retinas consisted of four forms with (V0, V1, V2, and V3) and two forms without (V1 and V3) the PLUS domain (PG-M+ and PG-M-, respectively). The four forms of PG-M+ were found in all samples examined, but the occurrence of the two PG-M- forms was regulated developmentally. Genomic analysis has revealed that the PLUS and CS-alpha domains are encoded by a single exon, and this exon has an internal alternative 5'-splice donor site, allowing alternative spliced forms that do not include the 3'-end of the exon. Sequences corresponding to the chicken PLUS domain (plus) were not found in mouse and human and may have disappeared during evolution. Sequence similarity suggests that the PLUS domain corresponds to the keratan sulfate attachment domain of aggrecan and that it has a distinct function in the chicken eye.

Aggrecans↗
PubMed2000

Evidence for two alternatively spliced forms of phospholipase C-beta2 in haematopoietic cells.

Alternatively spliced forms have been reported for several phospholipase C (PLC) isozymes, but not for PLC-beta2, the most abundant PLC-beta in platelets. PLC-beta2 cDNA cloned from the HL-60-cell cDNA library is 3543 bases long, coding for 1181 amino acids. Compared with the published sequence, a deletion of 45 nucleotides (2755-2799 nt, amino acids 864-878) was detected in platelet and leucocyte mRNA amplified by reverse transcription (RT) polymerase chain reaction (PCR) using primers corresponding to 1814-1838 nt (forward) and 3328-3352 nt (reverse). Amplification of genomic DNA using primers corresponding to 2575-2596 nt and 2864-2885 nt yielded a approximately 750 bp product; restriction analysis and sequencing revealed the 45-bp exon flanked by introns of 198 bp and 118 bp. Amplification of leucocyte and platelet cDNA using the same primers yielded products of approximately 310 nt and approximately 265 nt, with (PLC-beta2a) and without (PLC-beta2b) the 45-nt sequence. Thus, two alternatively spliced forms (1181 and 1166 amino acids) of PLC-beta2 are generated in haematopoietic cells. They differ in the carboxyl terminal sequence implicated in interaction of PLC-beta enzymes with Galphaq, particulate association and nuclear localization. We propose that the PLC-beta2 splice variants may be regulated differentially with distinct roles in signal transduction.

Alternative Splicing↗
PubMed1997

Differential expression of alternatively spliced pX mRNAs in HTLV-I-infected cell lines.

Human T cell leukemia/lymphotropic virus (HTLV) is a complex 9 kb human retrovirus with at least eight alternatively spliced mRNAs expressed from the 3' or pX region of the genome. These mRNAs allow for the expression of novel proteins from the previously recognized pX open reading frames I and II in addition to Tax, Rex and p21rex encoded from orf III and IV. These alternatively spliced messages have been detected using reverse-transcriptase polymerase chain reaction (RT/PCR) amplification in HTLV-I-transformed T cell lines as well as in peripheral blood mononuclear cells (PBMC) from infected patients with and without disease. To gain insight into the role of these alternatively spliced mRNAs in pathogenesis, we developed a semi-quantitative non-PCR-based RNase protection assay to detect and quantitate their presence in HTLV-I-infected cells. Analysis of RNA from HTLV-I-infected cells established from patients with adult T cell leukemia (ATL) as well as tropical spastic paraparesis/HTLV-I-associated myelopathy (TSP/HAM) and both IL-2-dependent and IL-2-independent HTLV-I-infected cell lines by RNase protection has confirmed the existence of all of the alternatively spliced messages in each cell line analyzed. However, the relative quantity of each message was significantly different among these lines suggesting that splice site utilization is an important viral regulatory pathway.

Adult↗
PubMed1998

Developmentally regulated alternative splicing in a novel synaptojanin.

Phosphatidylinositol phosphates (PIPs) perform central functions in signal transduction and membrane traffic. Synaptojanin is a PIP 5-phosphatase that is expressed in a brain-specific and a ubiquitous splice variants and is thought to constitute the major PIP 5-phosphatase in mammalian brain (Woscholski, R., Finan, P.M., Radley, E., Totty, N.F., Sterling, A.E., Hsuan, J.J., Waterfield, M. D., and Parker, P. J. (1997) J. Biol. Chem. 272, 9625-9628). We now describe synaptojanin 2, a novel isoform of synaptojanin that, similar to synaptojanin 1, contains an N-terminal SAC1-like sequence and a central 5-phosphatase domain but a distinct, unique C-terminal sequence. Transfection studies demonstrated that synaptojanin 2, like synaptojanin 1, is an active PIP phosphatase. An interesting feature of synaptojanin 1 is the presence of a long open reading frame in the 3' region of the brain mRNA that in non-brain tissues is joined to the coding region by alternative splicing, resulting in a shorter synaptojanin 1 form in brain and a longer form in peripheral tissues (Ramjaun, A. R., and McPherson, P. S. (1996) J. Biol. Chem. 271, 24856-24861). Although it exhibits no homology to synaptojanin 1 in this region, synaptojanin 2 also contains an open reading frame in the 3' region that is subject to alternative splicing. Similar to synaptojanin 1, alternative splicing of synaptojanin 2 is tissue-specific and creates a shorter isoform expressed in brain and a longer form in peripheral tissues. The similar alternative splicing of two homologous proteins in a region of non-homology raises the possibility of evolutionary convergence and supports the significance of the variants. Analysis of mRNAs from three brain regions at different developmental stages revealed that alternative splicing of synaptojanin 2 is a developmentally late event, occurring only after the first postnatal week after the generation of neurons and initial synaptogenesis.

Alternative Splicing↗
PubMed1993

An alternatively-spliced mRNA in the carboxy terminus of the neurofibromatosis type 1 (NF1) gene is expressed in muscle.

The gene for neurofibromatosis type 1 (NF1) was identified by positional cloning and found to contain two alternatively spliced exons. The first described alternatively spliced exon (exon 23a) is located within the GAP-related domain of the gene and inserts an additional 63 nucleotides into the NF1 mRNA. The second alternatively spliced exon (exon 48a) is located near the extreme carboxy terminus of the gene and inserts an additional 54 nucleotides into the mRNA. This second isoform, termed 3'ALT, was originally detected while screening a fetal brain cDNA library. Examination of its expression by reverse-transcribed RNA PCR demonstrates high level of expression in cardiac muscle, skeletal muscle and smooth muscle. Trace levels of expression are detected in brain and nerve. The 3'ALT isoform is expressed in fetal cardiac muscle, adult left ventricle and cardiac Purkinje cells. Further confirmation of the existence of this isoform was obtained by blotting the PCR products with a radiolabeled oligonucleotide entirely derived from sequences contained within exon 48a and by direct sequencing of the PCR products. Additionally, this isoform is expressed in muscle tissues from other vertebrate species. The expression of this isoform in muscle suggests that the NF1 gene may play additional tissue-specific roles in muscle development and signal transduction.

Alternative Splicing↗