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Bone morphogenetic protein-1 and a mammalian tolloid homologue (mTld) are encoded by alternatively spliced transcripts which are differentially expressed in some tissues.

Bone morphogenetic protein-1 (BMP-1) is a metalloprotease purified from extracts capable of inducing ectopic bone formation. In humans, it has a domain structure similar to that of the Drosophila dorsal-ventral patterning gene-product tolloid (Tld), but is considerably shorter. Here we show that, in humans and mice, alternatively spliced transcripts encode BMP-1 and a longer protein, designated mammalian tolloid (mTld), with a domain structure identical to that of Drosophila Tld. A third alternatively spliced product, in which a novel domain is inserted near the BMP-1 C terminus, is also reported. Low levels of transcripts for mTld were found in all adult human tissues surveyed, while BMP-1 transcripts were detectable in all adult tissues except brain. This differential expression was mirrored in embryonic mouse tissues where in situ hybridization found high levels of mTld transcripts, but was unable to detect BMP-1 transcripts, in the floor plate of the neural tube of the developing central nervous system. The third alternatively spliced form was not detected in adult human tissues. In situ hybridizations found punctate signals for all three forms localized to trophoblast giant cells in 17.5-day mouse placenta, with highest levels of expression, especially for BMP-1, near the maternal interface.

Alternative Splicing↗

Structure and alternative splicing of the rat 7-dehydrocholesterol reductase gene.

The enzyme 7-dehydrocholesterol reductase (Dhcr7) catalyzes the reduction of 7-dehydrocholesterol (DHC), the terminal reaction of the pathway of cholesterol biosynthesis. We report the isolation and characterization of the genomic DNA encoding rat Dhcr7 that contains nine exons and eight introns distributed over 15944 nucleotides (nts) and a consensus GT-AG at each exon/intron junction. Unexpectedly, we have found the occurrence of at least five isoforms of Dhcr7, designated as Dhcr7-AS (alternatively spliced)-1 (1474 nts), -2 (1595 nts), -3 (1602 nts), -4 (1723 nts) and -5 (1287 nts), which was believed to be caused by alternative usage of three 5' noncoding exons. Furthermore, Dhcr7-AS-1 was found to be differentially expressed in six tissues examined while Dhcr7-AS-2 was expressed mainly in liver and brain. Interestingly, human Dhcr7 gene in HepG2 cells produced no detectable isoform while mouse Dhcr7 gene in L929 cells produced three isoforms, suggesting a difference in alternative splicing between species. Thus, regulation of Dhcr7 through the combined mechanisms of tissue-specific transcription and differential alternative splicing appears unique among enzymes characterized from the entire post-lanosterol pathway in cholesterol biosynthesis.

Alternative Splicing↗

Humoral autoreactivity to an alternatively spliced variant of ICA512/IA-2 in Type I diabetes.

AIMS/HYPOTHESIS: The receptor tyrosine phosphatase like-protein ICA512/IA-2 occurs as a proteolytically-processed 65,000 Mr type 1 transmembrane glycoprotein in beta cells and is a major autoantigen of Type I (insulin-dependent) diabetes mellitus. We investigated whether alternative splicing could affect humoral autoreactivity to the molecule. METHODS: Genomic and cDNA sequence analysis showed the presence of a ICA512 variant in islets and lymphoid tissues with an in-frame deletion of exon 13 which produces a secreted form lacking aa 557-629 including the transmembrane domain (aa 577 to 600). The alternatively spliced protein is detectable by western blotting in normal islets and translated into a protein that is processed to a series of soluble forms of 25,000-35,000 Mr Radioimmuno-precipitation assays for anti-ICA512 autoantibodies were developed with the widely used ICA512.bdc construct (which has exon 13 deleted) and a series of full-length and modified ICA512/IA-2 molecules. RESULTS: The assays showed that ICA512.bdc and ICA512604-979 gave the best discrimination between diabetic and control sera. With ICA512604-979 a somewhat greater proportion of patients expressing antibodies were detected than with ICA512.bdc in the groups studied (70.5 % vs 63.2 % of prediabetic/new-onset and 25.0 vs 13.9% in patients with diabetes > 20 years). Conversely, a small proportion (3 % recent-onset and 6% > 20 years) had antibodies to ICA512.bdc but not ICA512(604-979). CONCLUSION/INTERPRETATION: Important epitopes lie within the exon 13 region and others can be generated by the alternative splicing. As the deltaexon 13 variant is probably secreted by the beta cell, it could be recognized by the cellular and humoral arm of the immune system in the absence of cellular damage.

Adolescent↗

Alternative splicing of dystrophin mRNA complicates carrier determination: report of a DMD family.

Carrier determination is important for genetic counselling in DMD/BMD families. The detection of altered PCR amplified dystrophin mRNA fragments owing to deletions, insertions, or point mutations has increased the possibilities of carrier determination. However, problems may occur because of alternative splicing events. Here we present a family with a DMD patient characterised by a deletion of exons 45 to 54. At the mRNA level we detected a corresponding altered fragment which served for carrier determination. The mother and the sister of the patient showed the same altered dystrophin mRNA fragment as the patient and are therefore carriers. In the mother two additional altered dystrophin mRNA fragments were detectable, obviously resulting from alternative splicing in the normal allele. The grandmother and two other related females of the patient possess only the normal mRNA fragment. In a further female we detected an altered fragment owing to an mRNA deletion of exon 44. This fragment is created either by alternative splicing or a new mutation. Therefore, the carrier status of this female is still ambiguous indicating problems in carrier determination by the method of dystrophin mRNA analysis.

Alternative Splicing↗

Gene structure, dual-promoters and mRNA alternative splicing of the human and mouse regulator of G protein signaling GAIP/RGS19.

Here we report the gene structure and transcription regulation of the human and mouse G protein-signaling regulator GAIP/RGS19. The GAIP/RGS19 gene is adjacent to and in an opposite orientation to the opioid-receptor-like receptor 1 (ORL1) gene. In both human and mouse, the GAIP/RGS19 gene is composed of seven exons. The first two exons are under the control of two different promoters and are alternatively employed to start the transcription of two 5' distinctive mRNAs. The two promoters appear to compete with and inhibit each other. We have also identified in mice an alternatively spliced short GAIP/RGS19 mRNA that lacks the exon 2 region and utilizes an ATG in exon 3 as its translation initiation codon. As a result, the short GAIP/RGS19 protein does not have the N-terminal 22 amino acid residues of a full-length isoform. GAIP/RGS19 alternative splicing patterns are differentially expressed in various tissues. The mRNA alternative splicing to produce multiple isoforms may play a significant role in regulating the function and selectivity of GAIP/RGS19.

Alternative Splicing↗

The mec-8 gene of C. elegans encodes a protein with two RNA recognition motifs and regulates alternative splicing of unc-52 transcripts.

Mutations in the mec-8 gene of Caenorhabditis elegans were previously shown to affect the functions of body wall muscle and mechanosensory and chemosensory neurons. Mutations in mec-8 also strongly enhance the mutant phenotype of specific mutations in unc-52, a gene that encodes, via alternative splicing of pre-mRNA, a set of basement membrane proteins, homologs of perlecan, that are important for body wall muscle assembly and attachment to basement membrane, hypodermis and cuticle. We have cloned mec-8 and found that it encodes a protein with two RNA recognition motifs, characteristic of RNA binding proteins. We have used reverse transcription-PCR and RNase protection experiments to show that mec-8 regulates the accumulation of a specific subset of alternatively spliced unc-52 transcripts. We have also shown with antibodies to UNC-52 that mec-8 affects the abundance of a subset of UNC-52 isoforms. We propose that mec-8 encodes a trans-acting factor that regulates the alternative splicing of the pre-mRNA of unc-52 and one or more additional genes that affect mechanosensory and chemosensory neuron function.

Alternative Splicing↗

In vivo expression of an alternatively spliced human tumor message that encodes a truncated form of cathepsin B. Subcellular distribution of the truncated enzyme in COS cells.

Cathepsin B is a lysosomal cysteine protease whose increased expression is believed to be linked to the malignant progression of tumors. Alternative splicing and the use of alternative transcription initiation sites in humans produce cathepsin B mRNAs that differ in their 5'- and 3'-untranslated ends. Some human tumors also contain cathepsin B-related transcripts that lack exon 3 which encodes the N-terminal signal peptide and 34 of the 62-amino acid inhibitory propeptide. In this study we show that one such transcript, CB(-2,3), which is missing exons 2 and 3, is likely to be a functional message in tumors. Thus, CB(-2,3) was found to be otherwise complete, containing the remainder of the cathepsin B coding sequence and the part of the 3'-untranslated region that is common to all previously characterized cathepsin B mRNAs in humans. Its in vitro translation product can be folded to produce enzymatic activity against the cathepsin B-specific substrate, Nalpha-benzyloxycarbonyl-L-Arg-L-Arg-4-methylcoumaryl-7-amide. Endogenous CB(-2,3) from the metastatic human melanoma cell line, A375M, co-sediments with polysomes, indicating that it engages the eukaryotic translation machinery in these cells. Epitope-tagged forms of the truncated cathepsin B from CB(-2,3) are produced in amounts comparable to the normal protein after transient transfection into COS cells. Immunofluorescence microscopy and subcellular fractionation show this novel tumor form of cathepsin B to be associated with nuclei and other membranous organelles, where it is likely to be bound to the cytoplasmic face of the membranes. This subcellular distribution was different from the lysosomal pattern shown by the epitope-tagged, full-length cathepsin B in COS cells. These results indicate that the message missing exons 2 and 3 is likely to be translated into a catalytically active enzyme, and that alternative splicing (exon skipping) could contribute to the aberrant intracellular trafficking of cathepsin B that is observed in some human cancers.

Alternative Splicing↗

Alternative splicing of N- and C-termini of a C. elegans ClC channel alters gating and sensitivity to external Cl- and H+.

CLH-3 is a meiotic cell cycle-regulated ClC Cl- channel that is functionally expressed in oocytes of the nematode Caenorhabditis elegans. CLH-3a and CLH-3b are alternatively spliced variants that have identical intramembrane regions, but which exhibit striking differences in their N- and C-termini. Structural and functional studies indicate that N- and C-terminal domains modulate ClC channel activity. We therefore postulated that alternative splicing of CLH-3 would alter channel gating and physiological functions. To begin testing this hypothesis, we characterized the biophysical properties of CLH-3a and CLH-3b expressed heterologously in HEK293 cells. CLH-3a activates more slowly and requires stronger hyperpolarization for activation than CLH-3b. Depolarizing conditioning voltages dramatically increase CLH-3a current amplitude and induce a slow inactivation process at hyperpolarized voltages, but have no significant effect on CLH-3b activity. CLH-3a also differs significantly in its extracellular Cl- and pH sensitivity compared to CLH-3b. Immunofluorescence microscopy demonstrated that CLH-3b is translationally expressed during all stages of oocyte development, and furthermore, the biophysical properties of the native oocyte Cl- current are indistinguishable from those of heterologously expressed CLH-3b. We conclude that CLH-3b carries the oocyte Cl- current and that the channel probably functions in nonexcitable cells to depolarize membrane potential and/or mediate net Cl- transport. The unique voltage-dependent properties of CLH-3a suggest that the channel may function in muscle cells and neurones to regulate membrane excitability. We suggest that alternative splicing of CLH-3 N- and C-termini modifies the functional properties of the channel by altering the accessibility and/or function of pore-associated ion-binding sites.

Alternative Splicing↗

Variable number tandem repeat in exon/intron border of the cystathionine beta-synthase gene: a single nucleotide substitution in the second repeat prevents multiple alternate splicing.

We studied a large number of individuals with respect to the 31-bp variable number tandem repeat (VNTR) in the cystathionine beta-synthase (CBS) gene. The number of repeats varies from 15-20, with 17 repeats the most common allele. Significantly, we found that the first repeat of the 31-bp VNTR originates 12 bp from the 5' end of exon 13 and extends 19 bp into intron 13. Since this VNTR spans across the exon-intron border, it can theoretically create multiple alternate splice sites. However, a substitution of g-->a at the exon-intron border is uniquely present in the second repeat, preventing alternate splicing at that site. While the g-->a substitution is absent from all subsequent 31-bp repeats, alternate splicing probably does not occur at those distal sites due to the lack of exon 13 sequences not contained in the repeats but needed for the binding of spliceosomes. Investigation of five individuals with normal plasma total homocysteine (tHcy) and five individuals with mild hyper-homocysteinemia shows that all have the g-->a substitution in the second repeat. Nonetheless, we speculate that the absence of this substitution may be found in rare individuals with normal CBS cDNA and unexplained hyperhomocysteinemia. Gene scanning and direct nucleotide sequencing were used to characterize the VNTR in 398 patients with premature coronary artery disease and 137 controls. Five alleles and 10 genotypes were found; 17/17 is the most prevalent genotype in our study population. The two other prevalent genotypes, 16/17 and 17/18, are associated with significantly decreased tHcy levels as compared to the 17/ 17 genotype, suggesting that the 16 and 18 repeats haplotype may be in linkage disequilibrium with regulatory elements which upregulate CBS gene transcription.

Adolescent↗

Alternative splicing is associated with decreased expression of the redox proto-oncogene thioredoxin-1 in human cancers.

Human thioredoxin-1 (Trx-1) is a small redox protein that is overexpressed in a number of human primary tumors, where it is associated with rapid cell proliferation and inhibited apoptosis. Mutation scanning denaturing high-performance liquid chromatography of Trx-1 mRNA in 58 human tumor cell lines found no evidence for changes in the base sequence of human Trx-1 mRNA. An alternatively spliced form of Trx-1 mRNA lacking exons 2 and 3 was found in 7 of the cell lines but it was not translated. The cell lines having the alternatively spliced Trx-1 mRNA had 73% lower total Trx-1 mRNA than the other cell lines, suggesting that alternative splicing may control the level of Trx-1 mRNA in some cancer cells.

Alternative Splicing↗

A novel hybrid alpha-tropomyosin in fibroblasts is produced by alternative splicing of transcripts from the skeletal muscle alpha-tropomyosin gene.

A single alpha-tropomyosin gene in the Japanese quail exhibits tightly controlled expression of multiple isoforms by an alternative splicing mechanism. We have isolated two full length cDNA clones, cC401 and cC402, from quail embryonic myofibers which differentiated in culture. cC402 is the major skeletal muscle alpha-tropomyosin, expressed in adult skeletal muscle and in embryonic muscle culture. cC401 exhibits a novel hybrid primary structure; smooth muscle structure at the carboxyl terminus is combined with skeletal muscle primary structure for the amino-terminal 90% of the protein. The cC401-type tropomyosin, unlike other smooth muscle or cytoskeletal tropomyosins, thus retains two muscle-type troponin-binding regions, for troponin I at amino acid residues 41-80 and for troponin T near amino acid residue 190, while switching to a different troponin binding site at residues 258-284. cC401-type mRNA is expressed at high levels in cultured skin fibroblasts and at low levels in cultured embryonic myoblasts and myofibers, but not in adult muscle, liver, or embryonic skin. A single quail genomic clone encodes both sets of alternative exons found in cC401 and cC402; the different transcripts from this gene share the same 5' ends. Two additional alpha-tropomyosin isoforms have been detected in quail tissues by S1 mapping experiments. Comparison of the cC401 protein with 11 other tropomyosin protein sequences shows that the quail alpha-tropomyosin gene has three different pairs of mutually exclusive exons which are alternatively spliced in nonrandom combinations in specific tissues. The implications of these findings are discussed in relation to mechanisms that regulate alternative splicing.

Amino Acid Sequence↗

[Molecular cloning for an alternatively splicing cDNA of human PKNOX1 gene and it's expression analysis].

Down's syndrome (DS) is the most common chromosomal abnormality in live born infants. The cloning and characterization of genes on HC21 are necessary steps for the understanding of the molecular basis of Down's syndrome. To search for new Down's syndrome related genes, we have used bioinformatics analysis and rapid amplification of cDNA ends to identify an alternatively splicing cDNA of human PKNOX1 in Down's syndrome critical region on the long arm of human chromosome 21. The alternatively splicing full length cDNA of human PKNOX1, named PKNOX1B, is 2 793 bp in length and encodes a 405 amino acid protein. Bioinformatical studies show PKNOX1B gene spans over 58 kb on chromosome 21q22.3 and contains 11 exons and 10 introns. The predicted molecule weight of PKNOX1B is 44.628 kDa, and the deduced iso-electric point is 6.28. Compared with PKNOX1 gene, PKNOX1B is 30 aa shorter at the C terminus than PKNOX1 owing to alternative splice between (10th exon and 11th exon) last two exons. PKNOX1B posses a same homeobox-domain as PKNOX1, so the isoform of PKNOX1 may be involved in the genetic control of development like other members of homeobox-containing gene family. RT-PCR results showed that PKNOX1B is expressed in all examined tissues except in marrow tissue. By Northern blot, PKNOX1 has three transcripts in adult testis, one about 5 kb, second about 2.9 kb, and third about 2 kb. The two larger transcript is expressed in all examined tissues, but the smallest transcript is only expressed actively in adult testis, so that it may play potential roles in spermatogenesis.

Alternative Splicing↗

A model system for activation-induced alternative splicing of CD45 pre-mRNA in T cells implicates protein kinase C and Ras.

Multiple isoforms of the protein tyrosine phosphatase CD45 are expressed on the surface of human T cells. Interestingly, the expression of these isoforms has been shown to vary significantly upon T-cell activation. In this report, we describe a novel cell line-based model system in which we can mimic the activation-induced alternative splicing of CD45 observed in primary T cells. Of the many proximal signaling events induced by T-cell stimulation, we show that activation of protein kinase C and activation of Ras are important for the switch toward the exclusion of CD45 variable exons, whereas events related to Ca(2+) flux are not. In addition, the ability of cycloheximide to block the activation-induced alternative splicing of CD45 suggests a requirement for de novo protein synthesis. We further demonstrate that sequences which have previously been implicated in the tissue-specific regulation of CD45 variable exons are likewise necessary and sufficient for activation-induced splicing. These results provide an initial understanding of the requirements for CD45 alternative splicing upon T-cell activation, and they confirm the importance of this novel cell line in facilitating a more detailed analysis of the activation-induced regulation of CD45 than has been previously possible.

Alternative Splicing↗

beta subunits modulate alternatively spliced, large conductance, calcium-activated potassium channels of avian hair cells.

Electrical tuning confers frequency selectivity onto sensory hair cells in the auditory periphery of frogs, turtles, and chicks. The resonant frequency is determined in large part by the number and kinetics of large conductance, calcium-activated potassium (BK) channels. BK channels in hair cells are encoded by the alternatively spliced slo gene and may include an accessory beta subunit. Here we examine the origins of kinetic variability among BK channels by heterologous expression of avian cochlear slo cDNAs. Four alternatively spliced forms of the slo-alpha gene from chick hair cells were co-expressed with accessory beta subunits (from quail cochlea) by transient transfection of human embryonic kidney 293 cells. Addition of the beta subunit increased steady-state calcium affinity, raised the Hill coefficient for calcium binding, and slowed channel deactivation rates, resulting in eight functionally distinct channels. For example, a naturally occurring splice variant containing three additional exons deactivated 20-fold more slowly when combined with beta. Deactivation kinetics were used to predict tuning frequencies and thus tonotopic location if hair cells were endowed with each of the expressed channels. All beta-containing channels were predicted to lie within the apical (low-frequency) 30% of the epithelium, consistent with previous in situ hybridization studies. Individual slo-alpha exons would be found anywhere within the apical 70%, depending on the presence of beta, and other alternative exons. Alternative splicing of the slo-alpha channel message provides intrinsic variability in gating kinetics that is expanded to a wider range of tuning by modulation with beta subunits.

Alternative Splicing↗

Posttranscriptional regulation of Id1 activity in cardiac muscle. Alternative splicing of novel Id1 transcript permits homodimerization.

The transcriptional regulatory protein Id, a negatively trans-acting protein with a helix-loop-helix motif that is expressed in many proliferating tissues early in development, continues to be expressed in postmitotic adult cardiac myocytes and vascular smooth muscle. Following the observation of a "doublet" band of 1.1 and 1.25 kilobases on Northern hybridizations of Id1 cDNA with mRNA isolated from both cardiac muscle and vascular smooth muscle cells, we identified and sequenced an alternatively spliced Id1 gene product containing an insert of 214 base pairs within the coding domain of the original Id1 cDNA. A protein with a molecular mass corresponding to that predicted by the Id1.25-kilobase mRNA sequence could be identified on immunoblots of cell lysates from neonatal and adult rat ventricular myocytes. The insert appears to be a "coding intron," based on the presence of intron-exon consensus sequences at the insert boundaries and the presence of the originally described Id1 carboxyl-terminal coding sequence immediately downstream from, and out of frame with, this insert. In contrast to Id1 and Id2, which do not form homodimers, the carboxyl-terminal sequence of this alternatively spliced Id1 transcript, termed Id1.25, permits homodimerization. Thus, alternative splicing of Id1 may allow for tissue-specific expression of Id1, while formation of homodimers could provide a post-translational mechanism to regulate the ability of Id1.25 to bind and inactivate E2A gene products.

Alternative Splicing↗

Developmental regulation of alternative splicing in the mRNA encoding Xenopus laevis neural cell adhesion molecule (NCAM).

The neural cell adhesion molecule (NCAM) is thought to play a role in the formation of the vertebrate nervous system. In mammals and chicken, it is known that more than 100 different forms of the NCAM protein can be generated by alternative splicing of one primary transcript and it is possible that these different forms have distinct biological functions. A large part of the diversity is generated by alternative mRNA splicing in two regions, called the pi and the muscle specific domain (MSD), that encode portions of the extracellular domain of the NCAM protein. In this report, we describe the tissue and developmental expression of the pi and MSD sequences in the amphibian, Xenopus laevis. Our experiments show that NCAM transcripts are present in all tissues examined including muscle, heart, liver, kidney, and brain. We have identified a 30-base exon, similar to the pi domain observed in mammals, that is not present in maternal NCAM RNA but appears in a subset of the NCAM mRNA population shortly after neural induction. At the predicted location of the MSD we have detected only two alternatively spliced exons, 3 bases and 15 bases in length. In no X. laevis tissue examined did we detect the two additional alternatively spliced exons which are present in the MSD region of mammalian and chicken NCAM RNAs. Finally, the analysis has revealed a dynamic and complex pattern of expression of alternatively spliced NCAM mRNAs during embryogenesis. High levels of expression of specific forms of NCAM RNA correlate with major morphogenic events such as neural tube formation and metamorphosis.

Amino Acid Sequence↗

Alternative splicing regulation impacts heart development.

SR proteins serve multiple roles in the posttranscriptional control of gene expression, including as regulators of alternative splicing. In this issue of Cell, Xu et al. (2005) demonstrate that a heart-specific knockout of one SR protein, ASF/SF2, produces cardiomyopathy and misregulation of specific alternative splicing events during early postnatal development.

Alternative Splicing↗

Alternative splicing affects the function and tissue-specific expression of the human constitutive androstane receptor.

BACKGROUND: The constitutive androstane receptor (CAR) plays a key role in the control of drug metabolism and transport by mediating the phenobarbital-type induction of many phase I and II drug metabolizing enzymes and drug transporters. RESULTS: We identified transcripts generated by four different alternative splicing events in the human CAR gene. Two of the corresponding ligand binding domain isoforms demonstrated novel functional properties: First, CAR(SV3), which is encoded by a transcript containing an lengthened exon 7, differentially transactivated target gene promoters. Second, CAR(SV2), which results from the use of an alternative 3' splice site lengthening exon 8, showed ligand-dependent instead of constitutive interaction with coactivators. Furthermore, alternatively spliced transcripts demonstrated a tissue-specific expression pattern. In most tissues, only transcripts generated by alternative splicing within exon 9 were expressed. The encoded variant demonstrated a loss-of-function phenotype. Correct splicing of exon 8 to exon 9 is restricted to only a few tissues, among them liver and small intestine for which CAR function has been demonstrated, and is associated with the induction of CAR expression during differentiation of intestinal cells. CONCLUSION: Due to their specific activities, CAR variant proteins SV2 and SV3 may modulate the activity of reference CAR(SV1). Furthermore, we propose that transcriptional activation and regulation of splicing of exon 9 may be coupled to ensure appropriate tissue- and differentiation state-specific expression of transcripts encoding functional CAR protein. Altogether, alternative splicing seems to be of utmost importance for the regulation of CAR expression and function.

Journal Article↗