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Results for “Alternative Splicing”

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PubMed2005

Alternative splicing and nonsense-mediated mRNA decay regulate mammalian ribosomal gene expression.

Messenger RNAs containing premature stop codons are generally targeted for degradation through nonsense-mediated mRNA decay (NMD). This mechanism degrades aberrant transcripts derived from mutant genes containing nonsense or frameshift mutations. Wild-type genes also give rise to transcripts targeted by NMD. For example, some wild-type genes give rise to alternatively spliced transcripts that are targeted for decay by NMD. In Caenorhabditis elegans, the ribosomal protein (rp) L12 gene generates a nonsense codon-bearing alternatively spliced transcript that is induced in an autoregulatory manner by the rpL12 protein. By pharmacologically blocking the NMD pathway, we identified alternatively spliced mRNA transcripts derived from the human rpL3 and rpL12 genes that are natural targets of NMD. The deduced protein sequence of these alternatively spliced transcripts suggests that they are unlikely to encode functional ribosomal proteins. Overexpression of rpL3 increased the level of the alternatively spliced rpL3 mRNA and decreased the normally expressed rpL3. This indicates that rpL3 regulates its own production by a negative feedback loop and suggests the possibility that NMD participates in this regulatory loop by degrading the non-functional alternatively spliced transcript.

Alternative Splicing↗

PubMed1989

Nucleotide substitutions within the cardiac troponin T alternative exon disrupt pre-mRNA alternative splicing.

The cardiac troponin T (cTNT) pre-mRNA contains a single alternative exon (exon 5) which is either included or excluded from the processed mRNA. Using transient transfection of cTNT minigenes, we have previously localized pre-mRNA cis elements required for exon 5 alternative splicing to three small regions of the pre-mRNA which include exons 4, 5, and 6. In the present study, nucleotide substitutions were introduced into the region containing exon 5 to begin to define specific nucleotides required for exon 5 alternative splicing. A mutation within the 5' splice site flanking the cTNT alternative exon that increases its homology to the consensus sequence improves splicing efficiency and leads to increased levels of mRNAs that include the alternative exon. Surprisingly, substitution of as few as four nucleotides within the alternative exon disrupts cTNT pre-mRNA alternative splicing and prevents recognition of exon 5 as a bona fide exon. These results establish that the cTNT alternative exon contains information in cis that is required for its recognition by the splicing machinery.

Animals↗

PubMed2000

Three different turkey luteinizing hormone receptor (tLH-R) isoforms I: characterization of alternatively spliced tLH-R isoforms and their regulated expression in diverse tissues.

Using combinations of reverse transcription-polymerase chain reaction (RT-PCR) and 5'- and 3'-rapid amplification of cDNA ends, three different, alternatively spliced, partial turkey LH receptor (tLH-R) cDNA isoforms were characterized from ovarian mRNA. The first cDNA (tLH-R(intact)) showed 98% and 72-75% similarity with chicken and mammalian LH-R sequences, respectively. The second cloned cDNA isoform (tLH-R(insert)) contained an in-frame TGA stop codon within an 86-base pair insertion that was located in the extracellular domain of the seven-transmembrane region. The tLH-R(insert) isoform could encode a truncated soluble protein isoform that lacked the transmembrane region. The third cDNA isoform truncated the transmembrane region (tLH-R(trunc)) and was derived by the deletion of the last exon by incomplete splicing. Generation of multiple transcripts by alternative splicing was elucidated by partial characterization of tLH-R genomic sequences. The differentially regulated expression of the tLH-R mRNA isoforms in nongonadal tissues and ovarian stromal tissues during various reproductive stages was quantified and analyzed by Northern blot and/or RT-PCR. Alternatively spliced tLH-R isoforms were differentially expressed in a tissue-specific manner in most of the tissues examined. The steady-state levels of tLH-R mRNA isoforms were relatively high in the hypothalamus and optic nerve and relatively low in the cortex, pituitary, and cerebellum when compared to levels in ovarian follicles. In nongonadal reproductive tissues, the steady-state levels of tLH-R mRNA isoforms were relatively high in the uterus and infundibulum and relatively low in the isthmus, oviduct, and magnum. In addition, in the nongonadal peripheral tissues, the steady-state levels of tLH-R isoforms were relatively high in the thyroid gland and relatively low in the spleen, adrenal gland, kidney, skin, bursa, and muscle. The present study suggests that the alternative splicing of LH-R transcripts occurs in a tissue-specific manner and has been evolutionarily conserved (similar results were obtained in chicken and swine). These results raise fundamental questions as to the function of LH-R isoforms in nongonadal tissues.

Alternative Splicing↗

PubMed2003

Therapeutic potential of antisense oligonucleotides as modulators of alternative splicing.

An estimated 60% of all human genes undergo alternative splicing, a highly regulated process that produces splice variants with different functions. Such variants have been linked to a variety of cancers, and genetic diseases such as thalassemia and cystic fibrosis. This Perspective describes a promising approach to RNA repair based on the use of antisense oligonucleotides to modulate alternative splicing and engender the production of therapeutic gene products.

Alternative Splicing↗

PubMed2001

Characterization of the human and mouse genes for the alpha subunit of type II prolyl 4-hydroxylase. Identification of a previously unknown alternatively spliced exon and its expression in various tissues.

Prolyl 4-hydroxylase (4-PH) catalyzes the formation of 4-hydroxyproline in -X-Pro-Gly- sequences and has a central role in the synthesis of all collagens. We report here on the cloning and characterization of the genes encoding the catalytic alpha(II) subunits of the human and mouse type II 4-PH [alpha(II)]2beta2 tetramers. The human and mouse genes are approximately 34.6 kb and 30.3 kb in size, respectively, and both consist of 16 exons. The translation initiation codons are located in exon 2, and the sizes of the exons consisting entirely of coding sequences are conserved in the two genes, varying from 54 to 240 bp, whereas the exons 1, containing the transcription initiation sites and 5' untranslated sequences, are 546 bp and 293 bp in the human and mouse, respectively. The sizes of the introns vary from 48 to 49 bp to over 8 kb in both genes. The 5' flanking regions contain no TATA box, but they and introns 1 contain several motifs that may act as transcription factor binding sites, including those for Sox9, which regulates chondrocyte-specific expression of collagens II, IX and XI. Unlike the human alpha(I) gene, the alpha(II) genes do not contain an alternatively spliced exon homologous to exon 9. However, a novel mutually exclusively spliced alternative exon 12a was identified in both genes. The nucleotide and amino-acid sequence identities between the 60-bp exon 12a and 66-bp exon 12b are about 35% and 45%, respectively, in both human and mouse genes. PCR analyses showed that both types of exon 12 are expressed in all tissues studied, except for adult leukocytes that expressed only mRNAs containing exon 12b sequences. Insect cell expression studies showed that a recombinant alpha(II) subunit containing amino acids coded by exon 12a associated with the beta subunit to form a fully active enzyme tetramer.

Alternative Splicing↗

PubMed2000

[Alternative splicing of de novo methyltransferase gene 3b in adult and newborn mice].

OBJECTIVE: To unravel the biological significance of the alternative splicing of de novo methyltransferase 3b, expression of the Dnmt3b gene in various tissues and developmental stages was investigated in postnatal mice. METHODS: RT-PCR and capillary electrophoresis were employed to analyze the alternative splicing pattern of Dnmt3b in tissues of newborn and adult mice. The results had been further reaffirmed by repeating and statistics analysis. Bioinformatics tools were used to predict the structure and hydrophobicity of the Dnmt3b exon10 coding sequence. RESULTS: Isoform with Dnmt3b exon10 was the abundant form in lung of newborn mice and in liver of both newborn and adult mice, while in other tissues of newborn and adult mice, the spliced isoform was presented as the predominant one. Peptide encoded by Dnmt3b exon10 was mainly random coil on the surface of Dnmt3b protein. CONCLUSIONS: The data demonstrate that the specific expression of Dnmt3b exists in tissues and developmental stages of postnatal mice. The alternative splicing of the exon 10 of Dnmt3b is possibly involved in the regulation of Dnmt3b's catalytic function. These results provide an insight into the developmental regulation and physiological function of the alternative splicing of the Dnmt3b gene.

Alternative Splicing↗

PubMed1994

Distribution of alternatively spliced chicken c-myb exon 9A among hematopoietic tissues.

The role of the c-myb proto-oncogene in cellular differentiation may be regulated in part by alternative splicing of its mRNAs. Previously, two forms of alternative splicing of the chicken c-myb gene between exons 9 and 10 were described: one form utilizes the entire 360 base pair (bp) exon 9A while a second form utilizes exon 9A' which consists of the 3' 150 bp of exon 9A. In this study the distribution among chicken hematopoietic tissues of these two forms of alternative splicing was determined by Northern blot analysis using a probe specific for exon 9A. RNA species of 4.2 kilobases (kb) and 4.4 kb which contain exon 9A' or exon 9A, respectively, were detected in each tissue tested. Quantitative analysis of the major 4.0 kb c-myb species and the c-myb species containing exon 9A and exon 9A' revealed that cells from yolk sac contained both the highest absolute and the highest relative levels of alternatively spliced c-myb mRNA, presumably because of the preponderance of immature erythroid cells in these preparations.

Alternative Splicing↗

PubMed2005

[Alternative splicing: a novel pharmacological target with wide therapeutic potential].

Alternative splicing is a process by which a single stretch of genomic DNA yields several mRNAs encoding different proteins. Once believed to be a marginal phenomenon, alternative splicing now appears to be widespread among higher organisms and to be behind a large repertoire of human diseases. It involves a flexible mechanism for selecting splice sites, based on regulatory sequences recognized by cognate trans-acting protein factors (stimulatory SR proteins, or their antagonists). This RNA-protein interaction provides two types of targets for therapeutic manipulation. Masking regulatory RNA sequences with an antisense strategy is the most obvious, and encouraging results are beginning to accrue. Our lab is currently developing an entirely new approach in which activating proteins are targeted by small chemical molecules. A large screening program has been conducted with the chemical library from the Curie Institute. Several molecules (all indole derivatives) were found to counter the stimulatory effects of individual activating proteins, and have been selected for further development.

Alternative Splicing↗

PubMed1994

Developmentally regulated alternative splicing generates a complex array of Drosophila para sodium channel isoforms.

The para locus encodes the predominant class of sodium channels expressed in Drosophila neurons. Previous sequence analysis of para cDNAs indicated the occurrence of alternative splicing at several sites within the open reading frame. Here we report a detailed analysis of this alternative splicing and its regulation during development. We have used a combination of RNA-PCR and sequence analysis to examine a 1.7 kilobase region of the para mRNA that encompasses the previously reported sites of alternative splicing. Five sites of alternative splicing were identified; 48 different splice variants could be generated by the differential exon usage observed. The number of splice forms and their relative frequency in vivo were characterized in RNA samples of both embryos and adults. The range of splice types was found to be much more diverse in adults than in embryos; of a total of 19 different combinations of alternative exons, 11 splice types were found in embryos and 18 in adults. Usage of some individual alternative exons changed during development; a newly identified exon, which is found in one of two forms either 24 or 30 base pairs long, was present in about 85% of para transcripts from embryos but only 7% of those in adults. These data suggest that a wide variety of subtly distinct Na channel isoforms are present in Drosophila, and that these may provide a range of voltage-gated sodium channel functions. Although multiple sodium channel genes have already been described in both Drosophila and mammalian systems, this study provides a clear indication that sodium channel variability may be much greater than previously thought.

Aging↗

PubMed2001

Alternative splicing and diversity of renal transporters.

The growing molecular identification of renal transporter genes is revealing that alternative splicing is common among transporters. In this paper, I review the physiological consequences of alternative splicing in some genes encoding renal transporters in which spliced isoforms have recently been identified. In some cases, the spliced isoforms resulted in nonfunctional proteins, which, however, possess a dominant negative effect on the cotransporter function, suggesting that the presence of such isoforms can be important in the functional regulation of the transporter. In most transporter genes, however, the spliced isoforms have been shown to be functional, resulting in a variety of physiological consequences, including, for example, changes in the polarization of isoforms to the apical or basolateral membrane, changes in pharmacological or kinetic properties, and changes in tissue distribution or intrarenal localization. In some cases, although the spliced isoform is functional, the consequence of splicing is still unknown. Different regulation among isoforms is an interesting possibility. Thus the diversity of several renal transporters is enhanced by alternative splicing mechanisms.

Alternative Splicing↗

PubMed2004

Complete genomic structure of the human nebulin gene and identification of alternatively spliced transcripts.

The giant nebulin protein is a fundamental structural component of the thin filaments of the striated muscle sarcomere. Nebulin binds to actin and the size of nebulin correlates with actin filament length, suggesting that nebulin may determine the length of the thin filaments during myofibrillogenesis. We have previously described the genomic organization of the 3' end of the nebulin gene (NEB), and identified 18 different NEB mutations in patients with autosomal recessive nemaline myopathy. Here we present the genomic organization of the entire nebulin gene, and the identification of numerous alternatively spliced mRNAs. The gene comprises 183 exons spanning 249 kb of the genomic sequence. The translation initiation codon is in exon 3, and the stop codon and the 3' UTR are in exon 183. There are four regions with alternatively spliced exons, that is, exons 63-66, 82-105, 143-144 and 166-177, giving rise to a number of different transcripts. The alternatively spliced exons 143-144 give rise to two different transcripts varying between muscle types and between muscles of different developmental stages. The alternatively spliced exons 166-177 express at least 20 different transcripts in adult human tibialis anterior muscle alone. Preliminary results show several transcripts in both of the two remaining alternatively spliced regions. Extensive alternative splicing of NEB may explain why nemaline myopathy patients with homozygous truncating mutations show expression of the carboxy-terminus of the nebulin protein contrary to expectations. The use of alternative transcripts might also explain why severe phenotypes are rare among patients with two truncating mutations.

Alternative Splicing↗

PubMed1995

Sodium current density correlates with expression of specific alternatively spliced sodium channel mRNAs in single neurons.

Elements within the first cytoplasmic loop of voltage-gated sodium channels have been implicated in regulating channel function. We have examined the role of alternative splicing within the first cytoplasmic loop of the Drosophila sodium channel gene para in regulating sodium current expression, using single-cell RT-PCR. In addition to a previously described exon (a), we identified a second exon in this region, designated exon i. Alternative splicing of exons a and i results in the expression of four para transcripts that are present individually or in combination within single neurons. Analysis of sodium current density and the pattern of para mRNA expression suggested that the presence of exon a was necessary though not sufficient for expression of sodium currents in cultured embryonic neurons. A similar pattern of alternative splicing of para mRNA was also evident in RNA isolated from whole embryos. Combined with our observation that the patterns of alternative splicing of para mRNA change during development, these findings suggest that neuronal sodium current expression in vivo, is also modulated by alternative splicing.

Alternative Splicing↗

PubMed2006

The expression and alternative splicing of alpha-neurexins during Xenopus development.

The neurexins are involved in the formation and function of synapses. Each of three genes encodes alpha- and beta-neurexins. Additional diversity (particularly of alpha-neurexins) arises from alternative splicing, resulting in a large number of protein isoforms, the significance of which is currently unclear. We have analysed alpha neurexin expression and alternative splicing during development of the frog Xenopus laevis. Surprisingly, each alpha-neurexin gene is expressed in immature oocytes. During embryonic development, each Xenopus neurexin (nrxn) gene has a distinct temporal expression pattern, with expression being almost exclusively within the neuroepithelium. The spatial expression of nrxnIalpha and nrxnIIalpha is similar in the developing CNS, with staining being observed in the optic cup and in dorsolateral regions of anterior neural tube, but not adjacent to the ventral midline. The pattern of nrxnIIIalpha expression is more restricted, in several domains of the anterior neural tube. In the forebrain, expression was confined to an area in the ventrolateral neural tube; nrxnIIIalpha was also expressed in the hindbrain and spinal cord. By stage 32, a period when synaptogenesis occurs, nrxnIIIalpha is expressed midway along the neural tube's dorso-ventral axis in the hindbrain and anterior spinal cord, at the site of the primary interneuron column. Because of the striking diversity of neurexin isoforms, we analysed alternative splicing of Xenopus transcripts during development and found examples of alternative splice variants of each neurexin. The data demonstrate differential regulation of the alpha neurexins with respect to the gene temporal and spatial expression and alternative splicing.

Alternative Splicing↗

PubMed1993

Neurexin III alpha: extensive alternative splicing generates membrane-bound and soluble forms.

The structure of neurexin III alpha was elucidated from overlapping cDNA clones. Neurexin III alpha is highly homologous to neurexins I alpha and II alpha and shares with them a distinctive domain structure that resembles a cell surface receptor. cDNA cloning and PCR experiments revealed alternative splicing at four positions in the mRNA for neurexin III alpha. Alternative splicing was previously observed at the same positions in either neurexin I alpha or neurexin II alpha or both, suggesting that the three neurexins are subject to extensive alternative splicing. This results in hundreds of different neurexins with variations in small sequences at similar positions in the proteins. The most extensive alternative splicing of neurexin III alpha was detected at its C-terminal site, which exhibits a minimum of 12 variants. Some of the alternatively spliced sequences at this position contain in-frame stop codons, suggesting the synthesis of secreted proteins. None of the sequences of the other splice sites in this or the other two neurexins include stop codons. RNA blot analysis demonstrate that neurexin III alpha is expressed in a brain-specific pattern. Our results suggest that the neurexins constitute a large family of polymorphic cell surface proteins that includes secreted variants, indicating a possible role as signaling molecules.

Alternative Splicing↗

PubMed2001

Expression of alternatively spliced estrogen receptor alpha mRNAs is increased in breast cancer tissues.

We previously identified 20 different alternatively spliced estrogen receptor alpha (ERalpha) mRNAs that have deletions in various combinations of exons in breast cancer cell lines using a novel 'Splice Targeted Approach' [J. Steroid Biochem. Mol. Biol. 72 (2000) 249]. In the current study, we compared the frequency of alternatively spliced ERalpha variant expression in 35 reduction mammoplasty and 38 breast cancer tissues with known ERalpha, ERbeta status using this highly specific 'Splice Targeted Approach'. A total of 16 different alternatively spliced variants were identified that have deletions in various combinations of exons in normal, as well as cancer tissues. However, not all 16 variants were present in every tissue. The frequency and type of variants in normal and cancer tissues was significantly different. Majority of normal tissues expressed only single exon deletion variants with the exception of those in combination with exon 2Delta and 7Delta. Tumor tissues, on the other hand, showed increased frequency of multiple exon deletion mRNAs (P<0.019). In addition, cancer tissues also showed an increased frequency of all variants compared with normal tissues (P<0.044). Among the 16 variants, the dominant negative variant, exon 3Delta, showed the most significant increase in cancer tissues (P=0.000032). Specifically, we detected four different mRNAs that have exon 2 deletion-exon 2Delta; 2 and 4Delta; 2 and 5Delta; and 2, 4-5Delta in various combinations in both normal and cancer tissues. A large number of normal tissues expressed two transcripts-exon 2Delta and 2, 4-5Delta. The multiple exon deletion 2, 4-5Delta were predominant in cancer tissues. Only the single exon 3 deletion variant, exon 3Delta, was detected in normal tissues. Cancer tissues showed the presence of a double exon deletion variant, exons 3 and 7Delta, in addition to exon 3Delta. A small fraction of normal tissues showed exons 2-3Delta mRNAs, whereas, cancer tissues showed increased frequency of exons 2-3Delta expression in addition to a triple exon deletion variant, exons 2-3, and 5Delta. The expression of exon 4Delta; or 4 and 7Delta or both was equivalent in normal and cancer tissues. Exon 5Delta transcripts were present at very low levels in both normal and tumor tissues. A small percentage of cancer tissues but not normal tissues showed exon 6Delta mRNA. The presence of single, double, triple and quadruple exon deletion mRNAs, exon 7Delta; 7 and 4Delta; 7, 3-4Delta; 7, 3-5Delta, respectively, were detected in normal as well as cancer tissues. Each normal and cancer tissue had a distinct profile of ERalpha wild type, ERbeta wild type and ERalpha splice variants. Heterogeneity in ER isoform profiles may result in variations in estrogen/anti-estrogen binding and activation/inactivation of estrogen-dependent genes, and, therefore, may have implications in the risk of developing breast cancer, survival with the disease and response to anti-estrogen, as well as other therapies.

Alternative Splicing↗

PubMed1990

Oncodevelopmental regulation of the alternative splicing of fibronectin pre-messenger RNA in human lung tissues.

Alternative splicing of fibronectin pre-mRNA at the ED-A region has been shown to be deregulated in malignant human liver tumors (F. Oyama et al., J. Biol. Chem., 264: 10331-10334, 1989). In order to extend this observation to other human cancers, we investigated the splicing patterns of fibronectin pre-mRNA at both ED-A and ED-B regions in normal, fetal, and cancerous lung tissues. Unlike in the liver, the ED-A+ mRNA was constitutively expressed in the lung irrespective of ontogenic or oncogenic stages. Although fetal tissues expressed the ED-A+ mRNA slightly more than did adult tissues, there was virtually no significant difference between malignant and nonmalignant tissues in the level of the ED-A+ mRNA. In contrast, significant expression of the ED-B+ mRNA was observed with fetal and cancerous tissues but not with normal adult tissues. Increased expression of the ED-B+ mRNA was associated with all types of lung cancer including adenocarcinoma, squamous cell carcinoma, small cell carcinoma, and large cell carcinoma. These results indicate that it is the ED-B, but not the ED-A, region where the alternative splicing of fibronectin pre-mRNA is oncodevelopmentally regulated in the lung. Our results also suggest that deregulation of the tissue-specific alternative splicing of fibronectin pre-mRNA is not a unique phenotype of liver cancer but rather a general feature of naturally occurring human cancer.

Animals↗

PubMed1994

Similar alternative splicing of a non-homologous domain in beta A4-amyloid protein precursor-like proteins.

The beta A4-amyloid protein precursor (APP) is a transmembrane glycoprotein that is the source of the characteristic beta A4-amyloid deposits found in Alzheimer brains. It is expressed in several isoforms generated by alternative splicing of exons 7, 8, and 15, of which the leukocyte-derived APP mRNAs lacking exon 15 are significantly expressed in non-neuronal tissues, but not in neurons. The recent finding of APP-like proteins prompted us to analyze alternative splicing of the nearest relative of APP, the amyloid protein precursor homologue (APPH) or amyloid precursor-like protein 2 (APLP2). We were able to show that there are two alternatively spliced inserts, i.e. the Kunitz protease inhibitor domain and a 12-amino-acid-encoding region on the NH2-terminal side of the transmembrane domain, which is part of the region of highest divergence between APP and APLP2/APPH. Analysis of the tissue-specific differential expression of the resulting four APLP2/APPH mRNA isoforms revealed that isoforms lacking the latter, non-homologous insert are highly expressed in non-neuronal tissues, but only weakly in neurons. While this resembles the tissue-specific alternative splicing of exon 15 of APP, expression of the Kunitz protease inhibitor-encoding exon of APLP2/APPH is abundant in both neuronal and non-neuronal tissues and thus differs from APP. Because of the similar regulation of alternative splicing of exon 15 of APP and the described APLP2/APPH insert, and because of structural similarities of the sequences and the predicted secondary structures, a functional homology of alternatively spliced isoforms of APP and APLP2/APPH is suggested.

Alternative Splicing↗

PubMed2006

A positive feedback loop couples Ras activation and CD44 alternative splicing.

The Ras signaling pathway is important in both cell proliferation and tumor progression. Alternatively spliced isoforms of CD44 containing variable exon 6 (v6) can serve as coreceptors for growth factor receptors that activate Ras. Here we use v6-specific small interfering RNA (siRNA) to investigate the role of CD44 alternative splicing in Ras signaling. We identify a positive feedback loop in which Ras signaling promotes CD44v6 splicing, and CD44v6 then sustains late Ras signaling, which is important for cell cycle progression. These results are the first demonstration of a positive feedback loop linking signaling-dependent alternative splicing to mitogenic progression.

Alternative Splicing↗