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Results for “Alternative Splicing”

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PubMed2002

Study of the 2719 mutant of the c-H-ras oncogene in a bi-intronic alternative splicing system.

C-H-ras proto-oncogene forms part of the signal transduction pathway of numerous external stimuli. This proto-oncogene is regulated by alternative splicing within its intron D due to the presence of the alternative intron D exon (IDX). The alternative splicing produces mRNA which encodes for the putative p19 protein, that lacks transforming potential. Herein, we demonstrated that SR proteins regulate the intron D splicing. Moreover, we studied the 2719 mutation of H-ras which has higher transforming potential than Ile12 and Val12 H-ras mutants and is also known to affect the 5' splice site of the IDX. However, here we show that the 2719 mutant can still be spliced when the upstream 5' splice-site is blocked. During these later studies, additionally, we generated a short 11 nucleotides 5' terminal exon that was fully defined and spliced in a bi-intronic pre-mRNA. The definition of this mini-exon was also addressed in this work.

Alternative Splicing↗
PubMed1995

Evidence for the presence of the alternatively spliced HLA-G mRNA forms in human mononuclear cells from peripheral blood and umbilical cord blood.

The HLA-G monomorphic, nonclassic HLA class I gene encodes the molecule that is the only major histocompatibility complex antigen expressed on cytotrophoblasts of placenta. This restricted expression on fetal tissue that is in contact with maternal tissue suggests that HLA-G products may play a role in maternofetal tolerance. We previously have demonstrated in first-trimester human trophoblasts a new alternatively spliced form of HLA-G mRNA lacking exon 4 (HLA-G4) and weak expression of HLA-G1 copy mRNA in adult peripheral blood lymphocytes. By using exon-specific HLA-G primers, we demonstrate in this work the presence of three additional alternatively spliced forms of HLA-G mRNA in human peripheral mononuclear cells (HLA-G2, HLA-G3, and HLA-G4). In umbilical cord blood, HLA-G transcription was observed at very low level and only three alternatively spliced forms were detected (HLA-G1, HLA-G2, and HLA-G3). In contrast, we did not revealed any HLA-G transcript in CD34+ fraction of cord blood cells.

Alternative Splicing↗
PubMed2003

Characterization of the human UBE3B gene: structure, expression, evolution, and alternative splicing.

E3 ubiquitin ligases target proteins for degradation by adding ubiquitin residues. We characterized full-length cDNAs for human and mouse UBE3B, a novel HECT-domain E3 ligase, and analyzed the structure of human UBE3B on chromosome 12q24.1. Alternative splicing of exon 20 of UBE3B generated two major transcripts. The 5.7-kb mRNA lacked exon 20 and encoded a full-length protein ligase, variant 1 (UBE3B_v1). A second transcript contained a 97-bp insertion encoded by exon 20 that introduced an in-frame stop codon. The predicted protein (UBE3B_v2) would lack the HECT domain and would be nonfunctional, since the HECT domain constitutes the active site for ubiquitin transfer. No alternative splicing was observed in this region of mouse UBE3B. Elimination of the HECT domain by alternative splicing has not been reported in any genes encoding HECT domain ligases and may represent a novel mechanism in regulating intracellular levels of functional HECT-domain ligases.

Amino Acid Sequence↗
PubMed2005

The MMA1 gene family of cancer-testis antigens has multiple alternative splice variants: characterization of their expression profile, the genomic organization, and transcript properties.

Previously, we reported the identification of MMA1A by screening for differential gene expression in two human melanoma cell lines displaying diverse metastatic behavior after subcutaneous inoculation into nude mice. Splice variant MMA1B, which also was identified through database homology searches, showed a high degree of similarity with the MMA1A for exons 1, 2, and 4, but was missing exon 3. Through extensive expression profiling among normal and tumor samples, both MMA1A and -1B were found to belong to the family of cancer-testis antigens. In this study, we identified four additional alternatively spliced MMA1 variants, named MMA1C, MMA1D, MMA1E, and MMA1F. Generally, these novel MMA1 transcripts differ from MMA1A in that exon 2 or exon 3 is enlarged because of the use of alternative splice sites in intron 2 of the MMA1 gene. Moreover, MMA1E also lacks exon 3, as was previously seen in MMA1B. In screening for expression of the novel MMA1 transcripts in normal and tumor tissues, we demonstrated that MMA1C, -1D, and -1E also are members of the cancer-testis antigen family. MMA1F was found in only one melanoma metastasis sample and therefore is believed to have been expressed incidentally. Furthermore, we comprehensively elucidated the genomic structure of the MMA1 gene and the characteristic features of the alternatively spliced MMA1 transcripts.

Alternative Splicing↗
PubMed2006

Human normal T lymphocytes and lymphoid cell lines do express alternative splicing variants of human telomerase reverse transcriptase (hTERT) mRNA.

Alternative splicing of telomerase reverse transcriptase (hTERT) mRNA is known to contribute to regulation of telomerase activity in normal and cancerous cells, however, previous studies indicated that normal human T and B cells exhibited constitutive expression of full-length hTERT mRNA without splicing variants and that activation of telomerase upon stimulation of the cells was due to the shuttling of hTERT protein from cytoplasm to nucleus [Proc. Natl. Acad. Sci. USA 96 (1999) 5147; J. Immunol. 166 (2001) 4826]. We found that typical variants of hTERT mRNA were widespread in human lymphocyte-derived cell lines and normal stimulated T cells. In activated T cells, induction of the full-length hTERT mRNA was coupled with increased hTERT protein expression and telomerase activity. Collectively, human normal and malignant lymphocytes, like other human cells, express splicing variants of hTERT mRNA and require transcriptional activation of the hTERT gene to acquire telomerase activity.

Alternative Splicing↗
PubMed1996

Alternative splicing of dystrophin exon 4 in normal human muscle.

The dystrophin gene is composed of at least 86 exons and the occurrence of several alternative splicing sites, mainly occurring in its 3' region, is a well recognised phenomenon. We have found that exon 4 can also be alternatively spliced in human skeletal and cardiac muscle.

Alternative Splicing↗
PubMed1992

Platelet-derived growth factor and alternative splicing: a review.

The mitogenic and chemotactic potency of platelet-derived growth factor (PDGF) has linked this polypeptide to the pathogenesis of several disease states including atherosclerosis and neoplasia. We have reviewed the recent literature on aspects relating to the structure, distribution and biology of PDGF and its high-affinity cell-surface and intracellular receptors. In addition to platelets, several normal and tumor cells secrete the mitogen in one or more of three possible dimeric configurations. Alternative splicing of exon 6 in PDGF A-chain RNA results in the formation of two protein species with different carboxy-termini. Initially, it was thought that the longer A-chain variant was processed only by transformed cells. However, recent evidence indicates that alternative splicing occurs in several cells which express the A-chain, including early Xenopus embryos. The functional significance of the exon 6 product, a highly basic region spanned by 18 amino acid residues (A194-211), is not precisely clear. We have summarized recent findings which implicate roles for A194-211 in the processing, secretion, and mitogenesis of the A-chain homodimer, nuclear transport signalling, and heparin binding. Thus, alternative splicing could play an important role in the modulation of the functional properties of the PDGF A-chain variants per se and in the complex interactive network of polypeptide growth factors and cytokines.

Alternative Splicing↗
PubMed2002

Regulation of fibronectin alternative splicing by a basement membrane-like extracellular matrix.

Hepatocytes are the source of plasma fibronectin (FN) which lacks the alternatively spliced EDI segment, distinctive of oncofetal FN. When hepatic or other epithelial cells are cultured on plastic, EDI inclusion is triggered. Here we report that EDI inclusion is inhibited when hepatic cells are cultured on a basement membrane-like extracellular matrix (ECM), demonstrating a new role for the ECM in the control of gene expression. The effect is duplicated by collagen IV and laminin but not by collagen I; is not observed with another alternatively spliced FN exon (EDII); and correlates with a decrease in cell proliferation, consistently with high EDI inclusion levels observed in many physiological and pathological proliferative processes.

Alternative Splicing↗
PubMed1995

c-jun inhibited the alternative splicing of neuron-specific amyloid precursor protein, but stimulated the non-neuron type one in P19 EC cells.

Three alternative splicing products of amyloid precursor protein (APP), APP770, 751 and 695, were detected in mouse embryonal carcinoma (EC) P19 cells by reverse transcriptase RNA polymerase chain reaction (RT-PCR). Alternative splicing of APP pre-mRNA in P19EC cells was remarkably changed by c-jun transformation. The relative ratio of APP770 encoding exons 7 and 8, non-neuron type, was increased by c-jun transformation, while that of APP 695 not encoding exons 7 and 8, neuron-specific one, was decreased. These results suggested that skipping of exons 7 and 8 was specifically blocked in c-jun transformed cells. APP 695, which increases in P19 EC cells under the culture conditions that induce the neuronal differentiation, did not increase in C2C5 cells under the same conditions, suggesting that c-jun transformed cells were not in the neuronal cell lineage and lost the ability to differentiate into neurons.

Alternative Splicing↗
PubMed1995

Block of the N-methyl-D-aspartate receptor by phencyclidine-like drugs is influenced by alternative splicing.

N-Methyl-D-aspartate (NMDA) receptors were expressed in Xenopus oocytes from injected mRNA. The presence of an alternatively-spliced insertion encoding 21 amino acids at the N-terminus of the NMDAR1 (NR1(111)) subunit, made homomeric assemblies of the receptor more sensitive to ketamine and MK-801 than receptors assembled from NMDAR1 subunits lacking this insert (NR1(011) and NR1(001)). The influence of this insert was maintained when NR1 subunits were co-expressed in heteromeric combinations with NR2B. The increased sensitivity of the receptors containing the insert (NR1(111)) was accompanied by a faster on-rate for drug action than was observed for receptors lacking the insert (NR1(011) and NR1(001)). Our results suggest that the action of phencyclidine-like drugs is influenced by the presence of Insertion I in the NMDA isoforms, generated by alternative splicing.

Alternative Splicing↗
PubMed1988

Monoclonal antibodies reveal evolutionary conservation of alternative splicing of the alpha A-crystallin primary transcript.

Because of their specificity and sensitivity, monoclonal antibodies are powerful tools in studies of protein structure and function. Therefore, we raised monoclonal antibodies against alpha A-crystallin and identified the antigenic determinant for two of these antibodies. Applying limited-digestion methods, we show that the region spanning residues 158-168 of alpha A-crystallin contains the epitope for the two monoclonal antibodies. These monoclonals were then used to study the occurrence in the lenses of different vertebrates of the elongated alpha Ains-crystallin chain, a product of alternative splicing. It appears that the mutational event resulting in the alternative splicing pattern of the alpha A-crystallin gene took place at least 70 million years ago. This alternative splicing phenomenon has been maintained in rodents and some other, unrelated mammals, but disappeared again in most mammalian lineages.

Animals↗
PubMed1994

Alternative splicing in the alpha 5(IV) collagen gene in human kidney and skin tissues.

Type IV collagen is a complex molecule composed of three alpha chains that can be of types alpha 1(IV) to alpha 5(IV). Each alpha chain contains an amino-terminal collagenous domain and a carboxyl-terminal noncollagenous (NC) domain consisting of 229 amino acids, which is involved in intermolecular cross-linking to construct the basement membrane network. Specific localization of alpha 5(IV) collagen in glomerular basement membranes (GBM) in the kidney indicates its crucial role for that construction. In human kidney cortex and skin RNA, we found an alternative splicing transcript which skips exon 50 of the alpha 5(IV) collagen gene using reverse transcription-polymerase chain reaction and direct sequencing of the PCR products. This alternative splicing introduces a stop codon at the first codon of exon 51, resulting in an mRNA encoding a protein lacking the 84 NC domain carboxylterminal amino acid residues encoded by exons 50 and 51. Recently, gene mutations affecting the alpha 5(IV) collagen NC domain have been reported in patients with X-linked Alport syndrome who display GBM destruction and progressive renal failure, which are usually milder in female patients. Therefore, the alternative splicing, if its truncated products are dominantly expressed in glomeruli, may cause GBM impairment and renal failure progression.

Aged↗
PubMed1994

Alternate splicing of human thromboxane synthase mRNA.

Two species of human thromboxane synthase (TXS) cDNA, called TXS-I and -II, were previously isolated (K. Ohashi, K.-H. Ruan, R. J. Kulmacz, K. K. Wu, and L.-H. Wang, 1992, J. Biol. Chem. 267, 789-793). TXS-II differs from TXS-I by a 163-bp deletion near the 3'-end of the coding region. Both types of TXS mRNA have now been demonstrated to be present in various blood and lung cultured cells. Analysis of the exon-intron boundaries of TXS genomic DNA revealed that the two mRNAs are generated via alternate splicing: TXS-II is produced by skipping an entire 163-bp exon which encodes the polypeptide segment containing the heme-binding cysteine conserved among other P450s. The mechanism by which alternate splicing occurs is probably due to the presence of a more powerful potential as the 3' acceptor site in the intron following the 163-bp exon. When expressed in baculovirus system, recombinant TXS-I catalyzed the formation of thromboxane A2 and 12-hydroxyheptadecatrienoic acid (HHT), whereas recombinant TXS-II did not synthesize thromboxane A2 or HHT. Alternate splicing of TXS RNA transcript thus may provide a mechanism for limiting cellular biosynthesis of thromboxane A2.

Alternative Splicing↗
PubMed1999

Identification, cloning and analysis of expression of a new alternatively spliced form of the metabotropic glutamate receptor mGluR1 mRNA1.

We have applied quantitative RT-PCR analysis to characterise relative levels of expression of the alternatively spliced mGluR1 mRNAs. This has also allowed us to identify and clone a new alternatively spliced form of the mGluR1 mRNA. The newly identified mGluR1f mRNA is expressed at moderate levels in rat brain, reaching its maximum in cortex. mGluR1f differs from the mGluR1a mRNA by deletion of a 35-bp fragment of the mGluR1a/alpha coding sequence and insertion of an 85-bp fragment, found only in mGluR1b/beta mRNA.

Alternative Splicing↗
PubMed2000

The intronerator: exploring introns and alternative splicing in Caenorhabditis elegans.

The Intronerator (http://www.cse.ucsc.edu/ approximately kent/intronerator/ ) is a set of web-based tools for exploring RNA splicing and gene structure in Caenorhabditis elegans. It includes a display of cDNA alignments with the genomic sequence, a catalog of alternatively spliced genes and a database of introns. The cDNA alignments include >100 000 ESTs and almost 1000 full-length cDNAs. ESTs from embryos and mixed stage animals as well as full-length cDNAs can be compared in the alignment display with each other and with predicted genes. The alt-splicing catalog includes 844 open reading frames for which there is evidence of alternative splicing of pre-mRNA. The intron database includes 28 478 introns, and can be searched for patterns near the splice junctions.

Alternative Splicing↗
PubMed2002

Translational repression of human matrix metalloproteinases-13 by an alternatively spliced form of T-cell-restricted intracellular antigen-related protein (TIAR).

Human matrix metalloproteinases-13 (HMMP13) shows a wide substrate specificity, and its expression is limited to pathological situations such as chronic inflammation and cancer. The coding sequence for HMMP13 is 86% identical to rat matrix metalloproteinases-13 (RMMP13); however, the regulation of HMMP13 and RMMP13 protein synthesis in renal mesangial cells is strikingly different. In human cells there is a discordance between HMMP13 mRNA levels and protein expression. Following IL-1 beta or TGF-beta(1) stimulation, HMMP13 mRNA levels increase significantly, whereas the protein expression is absent. This discordance is because of a species-dependent translational repression. In addition to the 3'-untranslated region of the matrix metalloproteinases-13 (MMP13) gene, the differential expression of an alternatively spliced transcript of the RNA-binding protein TIAR in human cell cultures is also critical for this post-transcriptional regulation. Transient expression of the 17-amino acid insert of the alternatively spliced form of TIAR reverses the HMMP13 mRNA silencing observed in human and primate species. In addition, co-transfection of the alternatively spliced form of TIAR and HMMP13 into Rat2 cells suppresses HMMP13 protein expression. Thus, we report for the first time that a species-dependent TIAR isoform plays a major role in the post-transcriptional silencing for HMMP13.

3' Untranslated Regions↗
PubMed2026

Disease-driven post-transcriptional alterations and alternative splicing in podocytes in focal segmental glomerulosclerosis.

Focal segmental glomerulosclerosis (FSGS) is a major cause of nephrotic syndrome and progression to end-stage renal disease, yet its molecular pathogenesis remains still incompletely defined. While transcriptional alterations in podocytes have been extensively characterized, the contribution of post-transcriptional regulatory mechanisms is poorly understood. Here, we combined a zebrafish podocyte-specific injury model with glomerulus-resolved transcriptomic profiling to dissect RNA regulatory alterations during FSGS progression. Integrated analyses of bulk RNA sequencing, small RNA profiling, and alternative splicing revealed pronounced, time-dependent remodeling of the glomerular transcriptome. We demonstrate that podocyte injury is associated with loss of key podocyte-specific proteins, activation of inflammatory pathways, remodeling of the extracellular matrix, and altered microRNA expression, such as miR-21 and miR-193. Moreover, we found that alternative splicing influences key podocyte gene expression, affecting genes critical for slit diaphragm integrity, actin cytoskeleton organization, and glomerular basement membrane stability. Isoform analyses identified FSGS-associated isoform switches in SRSF3 and EPB41L5. Importantly, these changes were also evident in glomeruli from FSGS patients, demonstrating that the zebrafish model recapitulates key molecular features of human disease and highlighting alternative splicing as a central regulatory mechanism in FSGS.

Animals↗