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PubMed2002

[p16INK4a exon 1 alpha knockout in mouse embryonic stem cells].

INK4a/ARF locus distinguishes itself by its unusual structure and function. It contains 2 overlapping genes with exons 1 alpha, 2 and 3 encoding p16INK4a and exons 1 beta, 2 and 3 encoding p19ARF. Mice with their exons 2 and 3 of the INK4a/ARF knocked out are viable and fertile but develop spontaneous tumors at an early age and highly sensitive to carcinogenic treatment. However, mice with their exon 1 beta knocked out, without interference the expression of p16INK4a, show almost the same phenotype as those with their exons 2 and 3 knocked out. This raises a question of whether the mouse p16INK4a plays a role in tumor suppression. To investigate this problem, a targeting vector pointing to p16INK4a exon 1 alpha with 1.5 kb Eco81 I/Acc II fragment as short arm and 5.9 kb Xba I/Xho I fragment as long arm was built. After linearlization and purification, the targeting vector was introduced into ES cells through electroporation. Thirty-seven G418- and gancyclovir-resistant colonies were picked out and one of them was confirmed as positive by Southern hybridization.

Animals↗

PubMed2002

[Transmission disequilibrium test of DRD4 exon III 48bp variant number tandem repeat polymorphism and tic disorder].

OBJECTIVE: To investigate whether DRD4 exon III48 bp variant number tandem repeat(VNTR) polymorphism is associated with tic disorder. METHODS: One hundred and twenty-two nucleus families were collected using Structured clinical interview for genetic study of Tourette syndrome and related disorders for family-based association analysis of tic disorder and DRD4 exon III 48bp VNTR polymorphism. One hundred and twenty-two trios were divided into two groups: tic disorder group (82 trios of Tourette syndrome or chronic tic disorder, TS&CT) and tic disorder accompanied with attention deficit and hyperactivity disorder (ADHD) group (40 trios of Tourette syndrome or chronic tic disorder accompanied with ADHD, TS&ADHD). Transmission disequilibrium test (TDT), in addition to polymerase chain reaction and VNTR technique were conducted in 122 trios. RESULTS: There exist 5 alleles at this polymorphic locus in this sample including DRD4 exon III 48bp 2-6 repeats. No transmission disequilibrium was found between DRD4 exon III 48 bp VNTR and tic disorder (chi square=7.44, P 0.12); however, when the sample was divided into two groups, transmission disequilibrium was noticed between the cases of TS&ADHD and this locus by overall allele-wise analysis (chi square=11.74, P 0.02), and there exists transmission disequilibrium exclusively between 5 or 6 repeats of 48bp VNTR(longer alleles) by allele-wise analysis (chi square=10.57, P 0.032, chi square=6.13, P 0.01). No transmission disequilibrium was seen between TS&CT and DRD4 exon III 48bp VNTR(chi square=3.38, P 0.50). CONCLUSION: The results of this study have revealed an association between the longer alleles of DRD4 exon III 48bp VNTR polymorphism and tic disorder accompanied with ADHD, thus suggesting a possible genetic risk factor of tic disorder accompanied with ADHD in Chinese.

Adolescent↗

PubMed2001

Screening for mutations in exons encoding the ligand-binding domain of the LDL receptor gene using PCR-CFLP and PCR-SSCP.

Primary hypercholesterolemia includes both monogenic disorders and polygenic conditions. Two well defined monogenic disorders are familial hypercholesterolemia (FH) and familial defective apolipoprotein (apo) B-100 (FDB). Both disorders convey high risk of premature coronary artery disease. FH and FDB are caused by mutations in LDL receptor and apo B-100 genes, respectively. In the present study, mutations in both genes in Thai subjects with primary hypercholesterolemia were screened. For apo B-100 gene, a common mutation R3500Q was screened. This mutation was not observed in the patients (n = 45). For LDL receptor gene, mutations in the exons encoding the ligand-binding domain were screened. By PCR-CFLP analysis, 18 abnormal CFLP patterns in exon 4, the hot spot for mutations, were found in patients (n=45). One of the DNA samples with abnormal CFLP patterns was previously identified and reported as a possible disease-causing mutation, namely D151Y. For the other exons, the screening technique was PCR-SSCP. Abnormal SSCP patterns in DNA samples from patients (n=20) were found as follows, two in exon 3, one in exon 5 and another one in exon 6. Further characterization by DNA sequencing and family studies for these abnormal patterns are underway.

Adult↗

PubMed1992

A novel exon mutation in the human beta-hexosaminidase beta subunit gene affects 3' splice site selection.

The molecular basis of a dramatically decreased steady state level of beta-hexosaminidase beta subunit mRNA in a patient with juvenile Sandhoff disease was investigated. Nucleotide sequence analysis of the HEXB gene coding for the beta subunit revealed two single base substitutions, one in exon 2 (A to G, a known polymorphism) and the other in exon 11 (C to T). Analysis of the beta subunit mRNA species demonstrated activation of a cryptic splice site in exon 11 as well as skipping of the exon. A transfection assay using a chimeric gene containing intron 10 flanked by cDNA sequences carrying the mutation confirmed that the single base substitution located at position 8 of exon 11 inhibits the selection of the normal 3' splice site. The results demonstrate a new type of exon mutation affecting 3' splice site selection.

Adult↗

PubMed1992

Exon skipping in purine nucleoside phosphorylase mRNA processing leading to severe immunodeficiency.

We report a defect in splicing of precursor messenger RNA (pre-mRNA) resulting from a naturally occurring mutation of the gene encoding purine nucleoside phosphorylase (PNP) in a patient with PNP-deficient severe combined immunodeficiency. This defects results from a G to T transversion at the terminal nucleotide of exon 2 within the 5' splice site of intron 2 and causes skipping of exon 2 during processing of PNP pre-mRNA. Translation of the misspliced mRNA results in a reading frameshift at the exon 1-exon 3 junction. The predicted polypeptide encoded by the aberrant mRNA is severely truncated, terminating at 31 amino acids. Only 4 residues at the NH2 terminus of the polypeptide correspond to PNP amino acids. Otherwise the translation product of the misspliced mRNA differs completely from PNP in amino acid sequence and has no PNP activity. The finding of exon skipping in PNP is the first report of a splicing defect resulting in PNP-deficient severe combined immunodeficiency. Analysis of the genomic context of the G-1 to T mutation of the 5' splice site lends support for the exon definition model of pre-mRNA splicing and contributes to the understanding of splice site selection.

Amino Acid Sequence↗

PubMed1992

Molecular diversity in amino-terminal domains of human calpastatin by exon skipping.

Calpastatin, a specific inhibitor of calpain, consists of a unique N-terminal domain (domain L) and four repetitive calpain-inhibition domains (domains 1-4). Calpastatin cDNA of human was reported to have two deletions in domains L and 1, as compared with that of pig and rabbit. We isolated human calpastatin genomic DNA clones, and the sequence analysis revealed seven exons for domain L and five exons for domain 1. Those deletions in the human cDNA were retained in its genomic DNA as exons 3 and 11. By the reverse transcription polymerase chain reaction method, three calpastatin cDNAs, full-length domains L and 1, and two natural mutants with deletions in either exon 3 or in both exons 3 and 5, were cloned from human fibroblast WI-38 cell line mRNA. Domain L was found to be rich in basic amino acid residues, especially for exon 3, and its N-terminal half was highly conserved among species. The isoelectric points (pI) of domain L and domains 1-4 were calculated to be 10.27 and 4.26-4.90, respectively. Moreover, human tissues and cell lines displayed different patterns of reverse transcription polymerase chain reaction products in agarose gel electrophoresis. Therefore, alternative splicing is most likely the cause for the molecular diversity, and the multiple isoforms are implicated for specific physiological roles.

Base Sequence↗

PubMed1992

Dominant thalassemia-like phenotypes associated with mutations in exon 3 of the beta-globin gene.

Mutations producing beta-thalassemia reach individual gene frequencies greater than .01 in malarial-endemic regions because beta-thalassemia trait individuals have increased genetic fitness over that of normal individuals. Exon 3 of the beta-globin gene has been relatively spared as a site of common beta-thalassemia mutations. Frameshifts caused by the loss of a single nucleotide and nonsense mutations produce beta-thalassemia trait when they occur in exons 1 and 2. In contrast, they usually produce chronic hemolytic anemia when present in exon 3. Certain missense mutations in exon 3 produce unstable globins and thalassemia intermedia with hemolysis in heterozygotes. Here we report two new mutations in exon 3 of the beta-globin gene. One is a single nucleotide deletion in codon 109 in a 78-year-old Lithuanian with chronic hemolytic anemia and features of thalassemia. It leads to an abnormal globin (beta Manhattan) that is elongated to 156 amino acids. The second is a CAG-CGG missense mutation at codon 127 that causes a Gln----Pro substitution (beta Houston) and a thalassemia intermedia with hemolysis in three generations of a British-American family. Although the clinical phenotypes of these two patients differed little, differences in globin-synthetic ratios were significant, presumably reflecting differences in the ability of each abnormal beta-globin to form alpha beta dimers. The paucity of high-frequency exon 3 mutations and their worldwide distribution is likely attributable to their phenotypic severity and loss of increased genetic fitness vis-a-vis malaria.

Aged↗

PubMed1990

Alpha 1-antitrypsin Null(isola di procida): an alpha 1-antitrypsin deficiency allele caused by deletion of all alpha 1-antitrypsin coding exons.

alpha 1-Antitrypsin (alpha 1AT) deficiency, a common hereditary disorder responsible for emphysema in Caucasians of northern European descent, is caused by single base substitutions, deletions, or additions in the seven exons (IA-IC and II-V), of the 12.2-kb alpha 1AT gene located on chromosome 14 at q31-32.3. Of the five known representatives of the "null" group of alpha 1AT-deficiency alleles (alpha 1AT genes incapable of producing alpha 1AT protein detectable in serum) evaluated at the gene level, all result from mutations causing the formation of stop codons in coding exons of the alpha 1AT gene. The present study identifies an alpha 1AT allele (referred to as "Null(isola di procida")) caused by complete deletion of the alpha 1AT coding exons. The Null(isola di procida) allele was identified in an individual with heterozygous inheritance of M(procida) (an allele associated with alpha 1AT deficiency) and a null allele. Although results of karyotypic analysis were normal, quantification of the copies of alpha 1AT genes in this individual revealed that the index case had only half the normal copies of alpha 1AT genes. Cloning and mapping of the Null(isola di procida) gene demonstrated a deletion of a 17-kb fragment that included exons II-V of the alpha 1AT structural gene. As a consequence of the deletion, the normal noncoding exons (IA-IC) were followed by exons II-V of the downstream alpha 1AT-like gene. Sequence analysis of the deletion demonstrated a 7-bp repeat sequence (GAGGACA) both 5' to the deletion and at the 3' end of the deletion, a 4-bp palindromic sequence (ACAG vs. CTGT) bracketing the deletion, and a novel inserted 4-bp sequence (CCTG) at the breakpoint, suggesting that the mechanism of the deletion may have been "slipped mispairing."

Alleles↗

PubMed1991

The alpha 1 (VIII) collagen gene is homologous to the alpha 1 (X) collagen gene and contains a large exon encoding the entire triple helical and carboxyl-terminal non-triple helical domains of the alpha 1 (VIII) polypeptide.

We recently cloned and sequenced alpha 1 (VIII) collagen cDNAs and demonstrated that type VIII collagen is a short-chain collagen that contains both triple helical and carboxyl-terminal non-triple helical domains similar to those of type X collagen (Yamaguchi, N., Benya, P., van der Rest, M., and Ninomiya, Y. (1989) J. Biol. Chem. 264, 16022-16029). We report here on the structural organization of the gene encoding the rabbit alpha 1 (VIII) collagen chain. The alpha 1 (VIII) gene contains four exons, whose sizes are 69, 120, 331, and 2278 base pairs. The first and second exons encode only 5'-untranslated sequences, whereas the third exon codes for a very short (3 nucleotides) stretch of 5'-untranslated sequence, the signal peptide, and almost the entire amino-terminal non-triple helical (NC2) domain (109 1/3 codons). Interestingly, the last exon encodes the rest of the translated region, including 7 2/3 codons of the NC2 domains, the complete triple helical domain (COL1, 454 amino acid residues), the entire carboxyl-terminal non-triple helical domain (NC1, 173 amino acid residues), and the 3'-untranslated region. This exon-intron structure is in stark contrast to the multi-exon structure of the fibrillar collagen (types I, II, III, V, and XI) genes, but it is remarkably similar to that of the type X collagen gene (LuValle, P., Ninomiya, Y., Rosenblum, N. D., and Olsen, B. R. (1988) J. Biol. Chem. 263, 18278-18385). The data suggest that the alpha 1 (VIII) and the alpha 1 (X) genes belong to the same subclass within the collagen family and that they arose from a common evolutionary precursor.

Amino Acid Sequence↗

PubMed1990

Alternative promoter and 5' exon generate a novel Gs alpha mRNA.

Several species of mRNA have been shown to encode the alpha subunit of the stimulatory GTP-binding regulatory protein, Gs alpha. The various Gs alpha mRNAs are generated through alternative splicing of a single precursor RNA and through the use of alternative acceptor splice sites. We now report the existence of a Gs alpha mRNA that uses a previously unidentified promoter and leading exon (termed exon 1'). In both the canine and human Gs alpha genes, exon 1' is located 2.5 kilobases 5' of exon 1. Exon 1' does not contribute an in-frame ATG, and thus its mRNA encodes a truncated form of Gs alpha. Initiation of translation is predicted to begin at an AUG in exon 2, as demonstrated both by in vitro translation and COS cell expression studies.

Animals↗

PubMed1989

Characterization of an alternative exon of the murine T cell receptor beta-chain. Pattern of expression and evolutionary conservation.

In this report, we characterize an alternate gene element of the murine TCR beta-chain. First, we have looked at the expression of the alternate exon, C beta 0, in normal T cell clones, as well as in fetal vs adult whole thymus. The C beta 0 exon is expressed in only 1% or less of TCR-beta messages in four of four mature T cell clones examined. C beta 0 is found at 10-fold higher levels in both fetal and adult thymus mRNA. Thus C beta 0 is developmentally regulated by T cells, although expression of the alternate exon is relatively constant from the fetal thymus to the adult thymus. Second, evolutionary conservation of the C beta 0 gene element was studied in both the rat and the human. The rat beta-locus contains a gene element highly homologous to the mouse C beta 0 gene, but the rat C beta 0 gene contains mutations in both splice sites that probably prevent the gene element from being spliced into mRNA. We have also sequenced the first exon of rat C beta 1, and find that the C beta 0 exon and the intron around C beta 0 are conserved between rat and mouse to the same level as the C beta 1 coding region. The intron around C beta 1, in contrast, shows the decrease in conservation between the two species that is expected for a noncoding region. Analysis of the putative C beta 0-containing region in the human reveals no sequences homologous to the C beta 0 gene element. Because the mouse is the only species that has conserved a functional C beta 0 gene, we conclude that the C beta 0 exon does not play a general role in T cell development.

Amino Acid Sequence↗

PubMed1989

Identification of alternatively spliced transcripts for human c-myb: molecular cloning and sequence analysis of human c-myb exon 9A sequences.

The murine c-myb gene has been recently shown to code for two protein products of 75kd and 89kd. The 89kd protein appears to be generated from an alternatively spliced mRNA which contains an additional stretch of 363 bases between exons 9 and 10. In this communication, we have examined whether similar alternatively spliced mRNAs of c-myb occur in human cells. Human c-myb exon 9A has been identified and sequenced in a cDNA clone (ML5) generated from the acute myeloid leukemic cell line ML-2. This alternatively spliced exon of c-myb has been found to contain the same number of nucleotides (363bp) as the corresponding mouse exon. Between murine and human exon 9A sequences, 81% sequence homology was found at the DNA level, while the homology at the predicted amino acid level was found to be 73%. A stretch of 14 amino acid residues at the junction of exons 9A and 10 have been found to be conserved between Drosophila and human sequences indicating that this region might perform an essential biological function which was deemed necessary through evolution.

Amino Acid Sequence↗

PubMed1994

Structure and expression of the human gene for the alpha subunit of prolyl 4-hydroxylase. The two alternatively spliced types of mRNA correspond to two homologous exons the sequences of which are expressed in a variety of tissues.

Prolyl 4-hydroxylase, an alpha 2 beta 2 tetramer, plays a central role in collagen synthesis as it catalyzes the formation of 4-hydroxyproline residues by the hydroxylation of proline in X-Pro-Gly sequences. We report here that the human gene for the catalytically important alpha subunit is more than 69 kilobase pairs and consists of 16 exons. The exons that encode solely protein sequences vary from 54 to 240 base pairs (bp), and the introns vary from 750 to more than 16,000 bp. The 133 bp of 5'-untranslated sequences of the mRNA are coded by two exons, and these sequences contain inverted repeats with a potential for stem-loop formation, which may be involved in translational control of the expression of this gene. The 5'-flanking region contains a TATa motif at -29 relative to the major transcription site but no CCAAT motif. The 5'-flanking region and the downstream sequences contain several motifs that may act as binding sites for various transcription factors. Evidence has previously been reported for a mutually exclusive alternative splicing of RNA transcripts of this gene. The present data indicate that the mutually exclusive sequences found in the mRNAs are coded by two consecutive, homologous 71-bp exons 9 and 10. These exons are identical in their first 5 bp and the overall identity between them is 61% at the nucleotide level and 58% at the level of the coded amino acids. Both types of mRNA were found to be expressed in all of the tissues studied, but in some tissues the type coding for exon 9 or 10 sequences was more abundant than the other type.

Alternative Splicing↗

PubMed1994

Genomic organization of the FMRFamide gene in Lymnaea: multiple exons encoding novel neuropeptides.

Based on the sequencing of genomic and cDNA clones, we were able to determine that the FMRFamide gene consists of five exons covering at least 20 kb and predict the presence of further novel peptides. The exons are alternatively spliced: exon I (hydrophobic leader sequence) to exon II (tetrapeptides) and exon I to exons III (heptapeptides), IV, and V. A cDNA clone encoding the heptapeptides is described and has also been shown to encode further novel peptides SKPYMRFamide, HDYMRFamide, and SSFPRYamide. Analysis of the right internal parietal nerve using mass spectrometry showed that the novel peptide SKPYMRFamide was cleaved from the precursor. This peptide excites neurons, suggesting a physiological function in the CNS.

Amino Acid Sequence↗

PubMed1994

Beta A4-amyloid protein precursor mRNA isoforms without exon 15 are ubiquitously expressed in rat tissues including brain, but not in neurons.

The beta A4-amyloid protein precursor (APP), the source of the beta A4-amyloid deposits found in Alzheimer brains, constitutes a family of transmembrane glycoproteins generated by alternative splicing. While exon 7 and exon 8 are well known to be alternatively spliced, APP mRNA isoforms without exon 15 were only recently identified in leukocytes and rat brain microglial cells and therefore denoted as L-APP mRNAs. In order to perform a detailed analysis of individual L-APP mRNA isoforms in perfused rat tissues, we developed a quantitative polymerase chain reaction assay from reverse transcribed RNA allowing us to analyze the alternatively spliced region in between exon 6 and 16. In all peripheral tissues examined, L-APP mRNA isoforms were detected comprising between 25% (skeletal muscle) and about 70% (aorta, pancreas) of total APP transcripts. All four possible APP mRNA isoforms without exon 15 were shown to exist, i.e. L-APP752, L-APP733, L-APP696, and L-APP677. L-APP expression in the central nervous system (approximately 4% of total APP mRNA) was then studied in more detail by analyzing different brain regions and tissues and primary cultured brain cells. The only cell type which was shown not to express L-APP mRNA to a detectable level is the neuronal cell. Ubiquitous expression of APP mRNAs lacking exon 15 except for neurons indicates an important function in non-neuronal cells and is especially remarkable since neurons are the primarily affected cells in Alzheimer's disease.

Alternative Splicing↗

PubMed1993

Mutually exclusive exon splicing of type III brain sodium channel alpha subunit RNA generates developmentally regulated isoforms in rat brain.

We have identified two exons of the type III rat brain sodium channel alpha subunit gene that undergo mutually exclusive alternative RNA splicing to produce mRNAs coding either for an isoform predominant in neonatal brain (IIIN) or a different isoform (IIIA) predominant in the adult. These exons are 92 base pairs in length and encode amino acids 203-232, which correspond to part of the S3 and most of the S4 transmembrane segments within domain I and the extracellular loop between them. Despite 21 nucleotide differences between the exons, only a single amino acid at position 209 is altered, specifying either aspartic acid (IIIA) or serine (IIIN). As evidence that these isoforms are generated via alternative splicing, we demonstrate that both exons are encoded within the type III gene. The nucleotide sequences of the neonatal and adult type III exons and the intervening intron as well as the developmental regulation of this splicing are nearly identical in the type II sodium channel gene. The conservation of the exon/intron structure and of the developmentally regulated patterns of expression of the type II and III sodium channel genes suggests that alternative mRNA splicing of this exon may play a substantial role in modulating sodium channel function during brain development by alteration of a single amino acid.

Animals↗

PubMed1993

Exon skipping caused by DNA recombination that introduces a defective donor splice site into the human glycophorin A gene.

We report here the pre-mRNA splicing of the human glycophorin Mz (HGpMz) gene altered by a defective donor splice site introduced into the third intron via the mechanism of gene conversion. We found that the directional transfer from HGpB(delta) to HGpA(alpha) of a 145-base pair silent homologous segment had resulted in HGpMz as an alpha-beta-alpha hybrid gene with a G-T transversion in the consensus GT motif of the 5'-donor splice site. Transcript analysis showed the presence in the Mz reticulocytes of three major glycophorin cDNA species of which two occurred as the shortened and aberrantly spliced products of HGpMz pre-mRNA lacking the sequences encoded by one and two exons, respectively. The skipping of exon III results in one HGpMz protein with 99 amino acids that bears the M and Sta blood group antigens, whereas the coincident skipping of both exon III and exon IV leads to the expression of a minor HGpMz protein with 86 amino acids. These results indicate that the translocated defective donor splice site not only causes uniform skipping of the upstream exon but also affects the processing of the downstream exon. Complementing our previous studies, the finding that the active and inactive splice sites can be transposed by DNA recombination and alternatively used to construct new glycophorin alleles reveals a novel mechanism for sequence diversification in human genes.

Amino Acid Sequence↗

PubMed1993

Alternative splicing of the chicken c-myb exon 9A.

The c-myb gene products are thought to be regulators of cellular replication and of differentiation and heterogeneity may underlie their multiple functions. To investigate the possible existence of heterogeneity we have examined the chicken c-myb mRNAs by Northern blot analysis and polymerase chain reaction amplification of cDNAs (RT-PCR). Northern blot analysis with the c-myb cDNA clone pSG3, which contains the entire open reading frame (ORF) plus 500 base pairs of 3' untranslated sequences (Gerondakis & Bishop, 1986), and genomic probes revealed c-myb RNA species of 4.3 kb in addition to the major 4.0 kb species. The 4.3 kb c-myb RNA contained the alternatively spliced exon 9A which is highly conserved and has also been detected in a minor 4.3 kb alternatively spliced c-myb mRNA in murine and human cells. Sequencing of the avian exon 9A revealed 360 bp exon homologous to that found in murine and human mRNAs, which contains three highly conserved sequence regions shared by all three species. RT-PCR demonstrated usage of exon 9A in five hematopoietic tissues and revealed an additional splicing variant which used the 3' portion of exon 9A. Northern blot analysis using splice site-specific oligonucleotide probes spanning the two splice junctions between exon 9 and 9A revealed four additional c-myb RNAs of 4.4 kb, 2.2 kb, 2.0 kb and 1.4 kb.

Alternative Splicing↗