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Results for “Alternative Splicing”

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PubMed1994

cis-regulatory sequences responsible for alternative splicing of the Drosophila dopa decarboxylase gene.

The Drosophila dopa decarboxylase gene, Ddc, is expressed in the hypoderm and in specific sets of cells in the central nervous system (CNS). The unique Ddc primary transcript is alternatively spliced in these two tissues. The Ddc CNS mRNA contains all four exons (A through D), whereas the hypodermal mRNA contains only three exons (A, C, and D). To localize cis-regulatory sequences responsible for Ddc alternative splicing, a Ddc minigene and several fusion genes containing various amounts of Ddc sequences fused to fushi tarazu (ftz) exon 1 were constructed and introduced into flies by P-element-mediated germ line transformation. We find that Ddc intron ab and exon B are sufficient to regulate Ddc alternative splicing, since transcripts of a minimal fusion gene containing most of Ddc intron ab and exon B are spliced to exon B in the CNS but not in the hypoderm. These results indicate that Ddc alternative splicing is regulated by either a negative mechanism preventing splicing to exon B in the hypoderm or a positive mechanism activating splicing to exon B in the CNS. Our previous data suggest that Ddc hypodermal splicing is the actively regulated splicing pathway (J. Shen, C. J. Beall, and J. Hirsh, Mol. Cell. Biol. 13:4549-4555, 1993). Here we show that deletion of Ddc intron ab sequences selectively disrupts hypodermal splicing specificity. These results support a model in which Ddc alternative splicing is negatively regulated by a blockage mechanism preventing splicing to exon B in the hypoderm.

Alternative Splicing↗

PubMed2002

Control of alternative splicing by antisense oligonucleotides as a potential chemotherapy: effects on gene expression.

Expression of alternatively spliced mRNA variants at specific stages of development or in specific cells and tissues contributes to the functional diversity of the human genome. Aberrations in alternative splicing were found as a cause or a contributing factor to the development, progression, or maintenance of various diseases including cancer. The use of antisense oligonucleotides to modify aberrant expression patterns of alternatively spliced mRNAs is a novel means of potentially controlling such diseases. However, to utilize antisense oligonucleotides as molecular chemotherapeutic agents, the global effects of these molecules need to be examined. The advent of gene expression array technology has now made it possible to simultaneously examine changes that occur in the expression levels of several thousand genes in response to antisense treatment. This analysis should help in the development of more specific and efficacious antisense oligonucleotides as molecular therapeutics.

Alternative Splicing↗

PubMed2004

Expression of alternatively spliced sodium channel alpha-subunit genes. Unique splicing patterns are observed in dorsal root ganglia.

Molecular medicine requires the precise definition of drug targets, and tools are now in place to provide genome-wide information on the expression and alternative splicing patterns of any known gene. DNA microarrays were used to monitor transcript levels of the nine well-characterized alpha-subunit sodium channel genes across a broad range of tissues from cynomolgus monkey, a non-human primate model. Alternative splicing of human transcripts for a subset of the genes that are expressed in dorsal root ganglia, SCN8A (Na(v)1.6), SCN9A (Na(v)1.7), and SCN11A (Na(v)1.9) was characterized in detail. Genomic sequence analysis among gene family paralogs and between cross-species orthologs suggested specific alternative splicing events within transcripts of these genes, all of which were experimentally confirmed in human tissues. Quantitative PCR revealed that certain alternative splice events are uniquely expressed in dorsal root ganglia. In addition to characterization of human transcripts, alternatively spliced sodium channel transcripts were monitored in a rat model for neuropathic pain. Consistent down-regulation of all transcripts was observed, as well as significant changes in the splicing patterns of SCN8A and SCN9A.

Alternative Splicing↗

PubMed1996

Alternative splicing of the Na(+)-Ca2+ exchanger gene, NCX1.

We describe an analysis of the NCX1 gene and show that various tissues express different alternatively spliced forms of the gene. Alternative splicing has been confirmed by the genomic analysis of the Na(+)-Ca2+ exchanger gene. We also describe the Drosophila Na(+)-Ca2+ exchanger as having many of the same structural characteristics of the mammalian exchangers and this locus as possibly undergoing alternative splicing in the same region that has been described in the NCX1 gene. The general structure of the exchangers is similar to that of the alpha-subunit of the (Na(+)+ K+)-A Pase. Finally, sequence comparison of the various molecules demonstrates that structural characteristics of these molecules are more strongly conserved than the primary sequence of these products.

Alternative Splicing↗

PubMed2006

[Pre-mRNA alternative splicing in cancer: functional impact, molecular mechanisms and therapeutic perspectives].

For most of the 25,000 human genes, the removal of introns by pre-messenger RNA splicing represents an essential step towards the production of functional messenger RNAs. Moreover, a majority of pre-messenger RNAs is alternatively spliced to yield different messenger RNAs. Cancer cells often display aberrant profiles of alternative splicing producing isoforms that can stimulate cell proliferation and migration or improve resistance to apoptosis. While mutations at splice sites or in splicing control elements have been identified, changes are also caused by alterations in the expression of proteins that affect splice site selection. Current challenges consist in documenting the functional diversity generated by alternative splicing and its contribution to different types of cancers. The development of innovative approaches aimed at reprogramming alternative splicing offers promising perspectives in cancer therapy.

Alternative Splicing↗

PubMed1994

Exclusion of an alternatively spliced exon in human ATP synthase gamma-subunit pre-mRNA requires de novo protein synthesis.

Tissue-specific isoforms of the mitochondrial ATP synthase gamma-subunit are generated by alternative splicing, and the heart/skeletal muscle-specific transcript lacks exon 9 in a cassette fashion (Matsuda, C., Endo, H., Hirata, H., Morosawa, H., Nakanishi, M., and Kagawa, Y. (1993) FEBS Lett. 325, 281-284; and Matsuda, C., Endo, H., Ohta, S., and Kagawa, Y. (1993) J. Biol. Chem. 268, 24950-24958). Here, we show that the endogenous heart-type mRNA is cell-specifically induced by the extracellular pH value in the HT1080 (human fibrosarcoma) and KYM-1 (human rhabdomyosarcoma) cell lines. In these cells, a low extracellular pH value induced exclusion of exon 9, and this induction was inhibited by cycloheximide treatment. In contrast, a high extracellular pH value resulted in mRNA transcription of the liver type, including exon 9, and did not require de novo protein synthesis. These results suggest that alternative splicing in the gamma-subunit pre-mRNA is regulated by on-off switching of protein synthesis of a trans-acting factor involved in this exon-excluding step. The signal of low pH value was blocked by the protein kinase inhibitor H-7 or Calphostin C (protein kinase C inhibitor), indicating the involvement of protein kinase C in the alternative splicing. This is a good model system for studies on the induction mechanism of alternative splicing in cultured mammalian cells, in which intracellular factors play a pivotal role for the exon-excluding step in the tissue-specific alternative splicing mechanism.

Alternative Splicing↗

PubMed1998

Identification of a novel alternatively spliced mRNA of murine pulmonary surfactant protein B.

An alternatively spliced mRNA of pulmonary surfactant protein B (SP-B) was identified in murine lung. Sequencing analysis revealed a 69 base-pair (bp) deletion at the beginning of exon 7 of SP-B, presumably the result of an alternative splicing event. Reverse transcription-polymerase chain reaction (RT-PCR) of mouse, rat, and rabbit lung RNA revealed the existence of full-length and the 69-bp deleted short form. Ribonuclease protection assay of the SP-B messenger RNA (mRNA) demonstrated expression of both isoforms in five strains of adult and fetal mice with different genetic backgrounds, as well as in rabbit, but not in human. Splice junction sequences in exon 6 and at the exon 7 splice boundary for the two isoforms are similar, including AG doublet identity, but sequence differences do not account for species variation in isoform abundance. The abundance of the short SP-B mRNA isoform was approximately 30% of total SP-B mRNA in mouse and rabbit. Analysis of precursor SP-B protein in mouse lung suggested that the two mRNA species are expressed as stable protein isoforms.

Alternative Splicing↗

PubMed1999

Localization of alternatively spliced NMDAR1 glutamate receptor isoforms in rat striatal neurons.

Alternative splicing of the mRNA encoding the N-methyl-D-aspartate (NMDA) receptor subunit NR1 changes the structural, physiologic, and pharmacologic properties of the resultant NMDA receptors. We used dual label immunocytochemistry and confocal microscopy to localize the four alternatively spliced segments of the NR1 subunit (N1, C1, C2, and C2') in rat striatal neurons. Striatofugal projection neurons and four populations of interneurons were studied. Projection neurons, which were identified by immunolabeling for calbindin and by retrograde tracing from the globus pallidus and the substantia nigra, were the only striatal neurons containing C1 segment immunoreactivity. Projection neurons were also C2 segment immunopositive, as were all other neuronal populations studied. Projection neurons were C2' segment immunonegative. In contrast, each of the interneuron types were labeled by the antibody to the C2' segment: nitric oxide synthase interneurons were labeled intensely, calretinin and parvalbumin neurons were labeled moderately strongly, and cholinergic neurons were also labeled but less strongly than the other types of interneurons. Parvalbumin interneurons showed distinct N1 segment immunolabeling, which was not found in other types of striatal neurons. Our results suggest that all striatal neurons studied synthesize NR1 subunit proteins, but the isoforms of the protein present in projection neurons and the several types of interneurons are distinct. This differential expression of NR1 isoforms may affect both neuronal function and selective vulnerability of neurons to injury.

Alternative Splicing↗

PubMed1996

Identification of alternative splicing form of Stat2.

We identified alternatively spliced forms of Stat2 in human and mouse mRNAs. The spliced forms are generated by reading through the intron between exon 20 and 21, which correspond to the region encoding SH2 domain. The spliced forms contain a stop codon in SH2 domain, and therefore give rise to a short form of Stat2 when the mRNAs are translated. The putative translated proteins lack half of the SH2 domain, the tyrosine phosphorylation site required for dimerization (or oligomerization) and DNA binding, and C-terminal activation domain. The significance of these spliced forms is discussed.

Alternative Splicing↗

PubMed1998

Characterization of MLH1 and MSH2 alternative splicing and its relevance to molecular testing of colorectal cancer susceptibility.

The phenomenon of alternative splicing in the DNA mismatch repair genes MLH1 and MSH2 was extensively investigated by coupled reverse transcription-polymerase chain reaction in different human tissues, including 42 mononuclear blood cell samples--31 obtained from familial colon cancer patients or their at-risk relatives and 11 from healthy blood donors--7 normal colonic mucosae, 4 established human cancer cell lines, 8 colorectal tumors, and one sample each of ileum, liver, muscle, thymus, breast, and EBV-transformed lymphoblasts. Several isoforms were observed for each gene. Products of MLH1 alternative splicing included mRNAs lacking alternative exons 6/9, 9, 9/10, 9/10/11, 10/11, 12, 16, and 17. For MSH2, products lacking exons 5, 13, 2 through 7, and 2 through 8 were identified. The levels of expression were found to vary among different samples. All isoforms were found in a relevant fraction (43-100%) of the mononuclear blood cell samples, as well as in other tissues. The splicing variants were also detected in normal colonic mucosa, with the exceptions of the MLH1 -6/9 and -10/11 and the MSH2 -13 isoforms. Germline mutations of MLH1 and MSH2 confer constitutional predisposition to the development of colorectal cancer and other neoplasms. A substantial proportion of the mutations identified so far involve alterations of the normal splicing process. Knowledge of the existence of multiple alternative splicing events, not caused by genomic DNA changes, is important for the evaluation of the results of molecular diagnostic tests based on RNA analysis.

Adaptor Proteins, Signal Transducing↗

PubMed2005

Variable alternative spliced exon (VASE)-containing and VASE-lacking neural cell adhesion molecule in the dorsal and ventral hippocampus of SAMP8 mice.

The neural cell adhesion molecule (NCAM) is involved in the development and synaptic plasticity of the brain. Differential splicing of the variable alternative spliced exon (VASE) in the fourth immunoglobulin domain can dramatically change the functional properties of NCAM. This paper discusses our analysis of the levels of different expression of VASE-containing NCAM (NCAM-VASE(+)) and VASE-lacking NCAM (NCAM-VASE(-)) mRNAs in the dorsal and ventral hippocampus of senescence-accelerated mice (SAM). We further investigated the individual level of NCAM-VASE(+) and NCAM-VASE(-) in relation to the capacity for spatial learning and memory as assessed by a Morris water maze task. The results showed that the levels of both NCAM-VASE(+) and NCAM-VASE(-) were increased significantly in dorsal but not ventral hippocampus in aged SAMP8 mice. The mean latencies to find the hidden platform of the learning task on the last day were positively correlated with the levels of NCAM-VASE(+) in the dorsal hippocampus of SAMP8, which reveals that the mice with high levels of NCAM-VASE(+) have poor learning performances. These results suggest that the up-regulation of NCAM-VASE(+) could be involved in the impairments of spatial learning and memory.

Aging↗

PubMed2004

How prevalent is functional alternative splicing in the human genome?

Comparative analyses of ESTs and cDNAs with genomic DNA predict a high frequency of alternative splicing in human genes. However, there is an ongoing debate as to how many of these predicted splice variants are functional and how many are the result of aberrant splicing (or 'noise'). To address this question, we compared alternatively spliced cassette exons that are conserved between human and mouse with EST-predicted cassette exons that are not conserved in the mouse genome. Presumably, conserved exon-skipping events represent functional alternative splicing. We show that conserved (functional) cassette exons possess unique characteristics in size, repeat content and in their influence on the protein. By contrast, most non-conserved cassette exons do not share these characteristics. We conclude that a significant portion of cassette exons evident in EST databases is not functional, and might result from aberrant rather than regulated splicing.

Alternative Splicing↗

PubMed1994

A novel glycosaminoglycan attachment domain identified in two alternative splice variants of human versican.

We have cloned an alternatively spliced glycosaminoglycan attachment domain (GAG-alpha) of human versican from cDNA libraries derived from U251MG glioma cells. Inserted carboxyl-terminal of the hyaluronan-binding region, this domain adds another 987 amino acids to the original versican (V1) core protein giving rise to the large V0 isoform with 3396 amino acids and 17-23 putative glycosaminoglycan attachment sites. The GAG-alpha domain is encoded by exon 7 of the human versican gene (Naso et al., J. Biol. Chem., 32999-33008). Sequence comparisons revealed a slight similarity to the alternative splice domain of PG-M, further supporting the notion that PG-M is the chicken homologue of versican. On immunoblots of a proteoglycan preparation from U251MG culture medium, anti-GAG-alpha antibodies reacted exclusively with the larger of two versican core proteins recognized by antibodies against the original GAG-beta domain. Using reverse transcription-polymerase chain reaction, we detected both the V0 and V1 isoforms in the cerebral cortex, aorta, intervertebral disc, liver, myometrium, and prostate, whereas keratinocytes exclusively expressed versican V1. In brain tissue, we identified a short versican variant (V2) including only the GAG-alpha domain. By expressing particular splice forms of versican, cells may control the hydration properties of their pericellular hyaluronan coat and thus could modulate interactions with the extracellular matrix or neighboring cells.

Alternative Splicing↗

PubMed2025

PRMT5 regulates alternative splicing of TCF3 under hypoxia to promote EMT and invasion in breast cancer.

Tumor hypoxia induced alterations in the epigenetic landscape and alternative splicing influence cellular adaptations. PRMT5 is a type II protein arginine methyltransferase that regulates several tumorigenic events in many cancer types. However, the regulation of PRMT5 and its direct implication on aberrant alternative splicing under hypoxia remains unexplored. In this study, we observed hypoxia-induced upregulation of PRMT5 via the CTCF in human breast cancer cells. Further, PRMT5-mediated symmetric arginine dimethylation H4R3me2s and H3R8me2s directly regulated the alternative splicing of TCF3. Under hypoxia, PRMT5-mediated histone dimethylation at the intronic conserved region (ICR) present between TCF3 exon 18a and exon 18b recruits DNMT3A, resulting in DNA methylation. DNA methylation at the TCF3-ICR is recognized and bound by MeCP2 resulting in RNA-Pol II pausing, promoting the recruitment of the negative splicing factor PTBP1 to the splicing locus of TCF3 pre-mRNA. PTBP1 promotes the exclusion of exon 18a which results in the production of the pro-invasive TCF3-18B (E47) isoform which promotes EMT and invasion of breast cancer cells under hypoxia. Collectively, our results indicate PRMT5-mediated symmetric arginine dimethylation of histones regulates alternative splicing of TCF3 gene thereby enhancing EMT and invasion in breast cancer hypoxia.

Humans↗

PubMed2000

Alternative splicing of intron 3 of the serine/arginine-rich protein 9G8 gene. Identification of flanking exonic splicing enhancers and involvement of 9G8 as a trans-acting factor.

9G8 protein belongs to the conserved serine/arginine-rich (SR) protein family, whose members exhibit multiple functions in constitutive and alternative splicing. We have previously shown that 9G8 primary transcripts are subjected to alternative splicing by excision/retention of intron 3 and to a tissue specific modulation. Because both 5'- and 3'-splice sites of intron 3 appear to be suboptimal in vertebrates, we tested the 9G8 intron 3 as a novel model system of alternative splicing. By using an in vitro approach and a mutational analysis, we have identified two purine-rich exonic splicing enhancers (ESE) located in exon 4 and a (GAA)(3) enhancer located in exon 3. These elements act in concert to promote efficient splicing activation both in vitro and in vivo. Titration experiments with an excess of exonic enhancers or SR-specific RNA targets strongly suggest that SR proteins are specifically involved in the activation process. Although ASF/SF2 was expected to interact the most efficiently with ESE according to the enhancer sequences, UV cross-linking coupled or not to immunopurification demonstrates that 9G8 is highly recruited by the three ESE, followed by SC35. In contrast, ASF/SF2 only binds significantly to the (GAA)(3) motif. S100 complementation experiments with individual SR proteins demonstrate that only 9G8 is able to fully restore splicing of intron 3. These results, and the fact that the exon 3 and 4 ESE sequences are conserved in vertebrates, strongly suggest that the alternative splicing of intron 3 represents an important step in the regulation of the expression of 9G8.

Alternative Splicing↗

PubMed1998

Characterization of a gene encoding a single-subunit bacteriophage-type RNA polymerase from maize which is alternatively spliced.

Single-subunit RNA polymerases belonging to the T3/T7 bacteriophage family are thought to be common throughout eukaryotes. We report the isolation and characterization of a nucleus-encoded single-subunit RNA polymerase gene from maize. This gene is highly homologous to other single-subunit RNA polymerase genes from Arabidopsis, Chenopodium. yeast and Neurospora crassa involved in organellar transcription. Genomic Southern analysis reveals 10 to 15 hybridising fragments, suggesting that maize contains a small gene family. The isolated gene contains 19 exons and its genomic structure is highly conserved when compared to the three Arabidopsis homologues. Unlike the case in Arabidopsis, intron-12 of the maize bacteriophage-type RNA polymerase gene is alternatively spliced. Quantitative RT-PCR revealed that the resultant alternatively spliced transcript represents approximately 21 to 26% of the total polymerase mRNA in maize coleoptiles. The orthologous wheat bacteriophage-type RNA polymerase is also alternatively spliced and the intron exhibits 78% identity to maize intron-12. The conservation in alternative splicing between wheat and maize and its absence from Arabidopsis suggest a functional requirement for the alternatively spliced product.

Alternative Splicing↗

PubMed1994

Cell-cycle dependent alternative splicing of the tenascin primary transcript.

Functionally different tenascin (TN) isoforms may be generated by alternative splicing of the TN primary transcript. In fact, it has been demonstrated that only the larger TN isoform containing the alternatively spliced region induces loss of focal adhesion in cultured cells and seems able to facilitate cell migration. Recent studies have shown that the higher molecular mass TN isoform is a marker of stromal cell proliferation in hyperplastic and neoplastic breast tissues. This finding prompted us to study the pattern of TN alternative splicing in proliferating and non-proliferating cultured fibroblasts. Here, we show that the mitogenic stimulation of fibroblasts with serum or cytokines leads to an early and striking modification in the steady-state levels of the two major TN mRNAs. We also show that de novo protein synthesis is not necessary for this modification, indicating that it is a "primary response" event. Similarly, mitogenic stimulation induces changes both in synthesis and accumulation of the different TN isoforms.

Alternative Splicing↗

PubMed2006

The types and prevalence of alternative splice forms.

The finding that eukaryotic gene structures are extremely complex prompted the development of new experimental techniques for the accurate measurement of transcription start site usage and of the expression of alternative splice forms. On the computational side, analyses of large databases of splice variants revealed differences in the length, motif composition and selection pressure between constitutive and alternatively spliced exons. Such features are being incorporated into novel computational tools for gene structure prediction. The result of these investigations is a continuously improving catalogue of alternative splice forms. How the expression of these alternative splice forms is regulated remains one of the major open questions.

Alternative Splicing↗