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PubMed1998

Identification of alternatively spliced transcripts encoding murine macrophage colony-stimulating factor.

We have isolated a novel cDNA encoding macrophage colony-stimulating factor (M-CSF) from a murine stromal cell line, ST2. The cDNA included an entire coding sequence of the M-CSF gene but contained an additional sequence of 140 base pairs (bp). Northern blot analysis demonstrated that other murine cell lines such as a fibroblastic cell line (L) and a stromal cell line (PA6) also expressed the transcripts corresponding to the clone. The nucleotide sequence analyses of the cDNA and the cloned M-CSF genome revealed that the 140-bp insertion sequence was part of intron 1 which separated exon 1 and exon 2: the former contained part of the amino acid residues of the signal sequence and the latter the rest of the signal sequence and the first 22 amino acid residues of the mature protein. The insertion of the 140-bp intron sequence not only changed the amino acid sequence of the signal peptide but also generated an in-frame termination codon. However, instead of the dysfunction of the original initiation codon, the 140-bp insertion sequence contained a putative ATG initiation codon that preserved the original open reading frame. Finally, we found that the cDNA directed the expression of a secreted and biologically active M-CSF protein when it was introduced into COS7 cells and M-CSF activity in the culture supernatants was measured using an M-CSF-dependent cell line. These results indicate the presence of an alternatively spliced M-CSF transcript which utilizes an alternate initiation codon in order to specify active M-CSF protein.

Alternative Splicing↗

PubMed2001

Preferential expression of an intact WRN gene in Werner syndrome cell lines in which a normal chromosome 8 has been introduced.

Werner syndrome (WS) is a premature aging syndrome caused by mutations in the WRN gene. All mutations of the WRN gene reported thus far are predicted to produce the truncated WRN proteins. The mRNAs that contain chain-termination mutations are supposed to be unstable due to degradation by nonsense-mediated mRNA decay (NMD). In the present study, we investigated the expressions of intact and nonsense-mutated WRN genes in Werner syndrome cell lines in which a normal chromosome 8 had been introduced by microcell fusion. We demonstrate here that the expression of the mutated WRN gene that produces nonsense mRNAs remains at low levels, resulting in the preferential expression of the intact WRN gene in the WS microcell hybrids. This result supports the idea that imperfect messages containing premature termination codons are eliminated by the RNA surveillance system, suggesting the significance of the NMD mechanism in the etiology of Werner syndrome.

Cell Line↗

PubMed1995

A novel human catalase mutation (358 T-->del) causing Japanese-type acatalasemia.

Japanese-type acatalasemia is characterized by the almost total loss of catalase activity in red cells and is often associated with ulcerating oral lesions. A splicing mutation in intron 4 of catalase gene has so far been a sole disease-causing mutation found in Japanese-type acatalasemic patients. We report here a novel single base deletion in the catalase gene causing Japanese-type acatalasemia. The patient was a 72 year-old Japanese male. His maternal grandmother and his father were first cousins. Molecular analysis using non-RI PCR-SSCP analysis combined with direct sequencing revealed a deletion of the 358th thymine in exon 4 of the patient's catalase gene. The proband was a homozygote and his mother and his three children were heterozygotes for this mutation. The frame shift caused by the nucleotide deletion should alter the downstream amino acid sequence and introduce a new termination codon TGA 43 bp 3' to the mutation. Although the truncated peptide chain consisted of 133 amino acid residues might be translated in the patient's tissue, such an aberrant protein is expected to be extremely unstable and have no catalytic function at all. Our results suggest that Japanese-type acatalasemia is heterogeneous.

Acatalasia↗

PubMed2000

Anovel catalase mutation (a GA insertion) causes the Hungarian type of acatalasemia.

Acatalasemia, a deficiency of enzyme catalase, is an autosomal recessive syndrome with an incidence of 5:106 in Hungary. We have examined the first Hungarian acatalasemic family for the disease-causing mutation. All exons of the catalase gene were screened by PCR-SSCP, PCR-heteroduplex, and nucleotide sequence analysis. The heteroduplex formation detected in exon 2 was verified by nucleotide sequence analysis. We found a GA insertion at nucleotide position 138, increasing the GA repeat number from 4 to 5. This GA insertion caused a frameshift in the amino acid sequence from position 68 to 133 and generated a TGA terminating codon at amino acid position 134. This truncated protein lacks the essential amino acid (histidine 74) in the active center. This finding can explain the decreased blood catalase activity in the Hungarian acatalasemic family.

Acatalasia↗

PubMed1997

Cholesteryl ester storage disease: relationship between molecular defects and in situ activity of lysosomal acid lipase.

The molecular defects in the LIPA gene encoding the lysosomal acid lipase (LAL) were investigated in two unrelated patients affected with cholesteryl ester storage disease (CESD), an autosomal recessive disorder associated with LAL-deficient activity. In cell lysates from both patients there was a severely reduced LAL activity. In a female patient, nucleotide sequencing of amplified LAL genomic DNA or reverse-transcribed mRNA demonstrated that she was a compound heterozygote for two previously reported mutations, a G --> A transition at position -1 of the exon 8 splice donor site, resulting in skipping of the complete exon 8, and a C923 --> T substitution leading to the replacement of His274 to Tyr. The second, male CESD patient was heterozygous for the splice junction mutation and a yet undescribed C --> T substitution at position 233, which introduces a premature in-frame termination codon. The functional consequences of these genetic alterations were evaluated for the first time by studying the catabolic turnover of radiolabeled cholesteryl oleate in intact cells. A lower in situ residual LAL activity was found in cells carrying the stop codon mutation than in cells having the His274 --> Tyr substitution. Since the severely reduced LAL activity was seen in cells from an adult patient with a mild CESD, we conclude that there is no simple direct correlation between the LAL molecular lesions and the biochemical and clinical phenotypes.

Adult↗

PubMed1993

Molecular cloning, cDNA sequence, and chromosomal assignment of the human radixin gene and two dispersed pseudogenes.

Radixin is a cytoskeletal protein that may be important in linking actin to the plasma membrane. Recent cloning of the murine and porcine radixin cDNAs revealed a protein highly homologous to ezrin and moesin. We have cloned and sequenced the human radixin cDNA and found the predicted amino acid sequence for the human protein to be nearly identical to those predicted for radixin in the two other species. By Southern analyses of Chinese hamster x human somatic cell hybrid DNA and of PCR products derived from hybrids, the coding gene (RDX) was mapped to 11q. Fluorescence chromosomal in situ hybridization with a cDNA plasmid further localized this gene to band 11q23. However, PCR amplification with "radixin-specific" primers on the hybrid DNA panel yielded an additional, very similar DNA sequence that was further characterized by direct sequencing of PCR products. This sequence represents a truncated version and the respective locus (RDXP2) was assigned to Xp21.3. Furthermore, by employing a different set of primers, a third sequence was found that was 90% identical to the radixin sequence but contained termination codons and seemed to lack introns. This pseudogene (RDXP1) was mapped to 11p by Southern and PCR analyses.

Amino Acid Sequence↗

PubMed1993

Complete structure of the human Gc gene: differences and similarities between members of the albumin gene family.

The sequence of the human Gc gene, including 4228 base pairs of the 5'-flanking region and 8514 base pairs of the 3' flanking region (55,136 in total), was determined from five overlapping lambda phage clones. The sequence spans 42,394 base pairs from the cap site to the polyadenylation site, and it reveals that the gene is composed of 13 exons, which are symmetrically placed within the three domains of the Gc protein. The first exon is partially untranslated, as is exon 12, which contains the termination codon TAG. Exon 13 is entirely untranslated, but contains the polyadenylation signal AATAAA. Ten central introns split the coding sequence between codon positions 2 and 3 and between codon positions 3 and 1 in an alternating pattern, exactly as has been observed in the structure of the albumin and alpha-fetoprotein genes. The Gc gene has several distinctive features which set it apart from the other members of the family. First, the gene is smaller by two exons, which results in a protein some 130 amino acids shorter than albumin or AFP. This decrease in size may result from the loss of two internal exons during the evolutionary history of the Gc gene. Second, exons 6, 8, 9, and 11 are smaller than their counterparts in albumin or AFP by a total of 8 codons (1, 4, 1, and 2, respectively). Although the mRNA and protein expressed from the Gc gene are significantly smaller, the gene itself is about 2.5 times larger than the other genes of the family.(ABSTRACT TRUNCATED AT 250 WORDS)

Albumins↗

PubMed1993

The human carboxyl ester lipase-like (CELL) gene is ubiquitously expressed and contains a hypervariable region.

In this paper we characterize the human carboxyl ester lipase-like (CELL) transcript. An analysis of the tissue distribution of the expression of the gene shows that it is expressed in low amounts in all tissues analyzed. This is in contrast to its closely related and functional gene, the carboxyl ester lipase (CEL) gene, which is expressed only in human lactating mammary gland and pancreas. The primary structure of the cDNA encoding the carboxyl ester lipase-like transcript has been determined. The average length of the cDNA is 1214 bases. This sequence includes several termination codons in all three reading frames. The longest open reading frame with the same start of translation as that of the CEL transcript could encode a 59-amino-acid-long peptide, presumably without any function. The CELL gene may have arisen as a result of a gene duplication of the CEL gene followed by deletions and point mutations. However, the mutations are unevenly distributed. In the first three exons no mutations are found compared to the corresponding exons of the CEL gene. On the other hand, in the next exon several point mutations and a 2-base insertion are found and are present in all individuals analyzed. A hypervariable region present in the last exon of the CELL gene is also characterized. Several allelic variants can be resolved by polymerase chain reaction amplification of this region followed by sequencing using an automated laser fluorescent sequencer.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗

PubMed1994

Molecular analysis of functional and nonfunctional genes for human ferrochelatase: isolation and characterization of a FECH pseudogene and its sublocalization on chromosome 3.

A pseudogene related to the functional gene (FECH) for the heme biosynthetic enzyme ferrochelatase (ferroheme-protolyase; EC 4.99.1.1.) was isolated from a human genomic library using a ferrochelatase cDNA hybridization probe. The pseudogene shows > 80% overall nucleotide sequence identity to the functional gene (including the 3' untranslated region and polyadenylation signals) but contains no intronic sequences in the region corresponding to the open reading frame of expressed ferrochelatase. Furthermore, the pseudogene sequence contains small deletions and insertions creating frameshifts and numerous termination codons, indicating that it does not encode a functional polypeptide. Northern blot analysis using pseudogene-specific probes failed to demonstrate transcripts in samples of human erythroid cell RNA in which ferrochelatase mRNA was readily detected. Southern blot experiments using restriction endonuclease-digested human genomic DNA probed either with ferrochelatase-specific cDNA fragments or pseudogene-specific genomic sequences confirmed the presence of distinct loci for the expressed and nonfunctional genes, respectively. Localization of the human ferrochelatase pseudogene to 3p22-p23 was determined by fluorescent metaphase chromosomal hybridization in situ using three genomic clones in lambda EMBL3 spanning a contiguous region of approximately 30 kb. This newly identified locus, distinct from the expressed FECH gene, on 18q22, is characteristic of a processed human pseudogene. The existence of the ferrochelatase pseudogene has practical implications for the molecular analysis of mutations responsible for erythropoietic protoporphyria in man.

Amino Acid Sequence↗

PubMed1994

Cloning and molecular characterization of the Chinese hamster ERCC2 nucleotide excision repair gene.

The Chinese hamster ERCC2 nucleotide excision repair gene, encoding a presumed ATP-dependent DNA helicase, was cloned from the V79 cell line, and its nucleotide sequence was determined. The approximately 15-kb gene comprises 23 exons with a 2283-base open reading frame. The predicted 760-amino-acid protein is 98% identical to the human ERCC2/XPD (760 amino acids), 51% identical to the Saccharomyces cerevisiae RAD3 (778 amino acids), and 54% identical to the Schizosaccharomyces pombe rad15 (772 amino acids) proteins. The promoter region of the hamster ERCC2 gene contains a pyrimidine-rich stretch (42 nucleotides, 88% C+T) similar to sequences found in the promoter regions of two other nucleotide excision repair genes, a GC box, a putative alpha-Pal transcription factor binding site, and two CAAT boxes. There is no apparent TAATA box. No consensus polyadenylation sequence (AATAAA or its variants) was found within 663 bases 3' of the translation termination codon.

Adenosine Triphosphatases↗

PubMed1994

A homozygous nonsense mutation in the beta 3 chain gene of laminin 5 (LAMB3) in Herlitz junctional epidermolysis bullosa.

Herlitz junctional epidermolysis bullosa (H-JEB) is a severe autosomal recessive disorder characterized by blister formation within the dermal-epidermal basement membrane. Based on immunofluorescence analysis recognizing laminin 5 epitopes (previously known as nicein/kalinin), the genes for this lamina lucida protein have been proposed as candidate genes in H-JEB. In this study, we examined the gene encoding the beta 3 polypeptide chain of laminin 5 (LAMB3) by Northern hybridization and RT-PCR analysis of keratinocyte mRNA from a proband in a family with H-JEB. Northern analysis revealed markedly reduced levels of the laminin beta 3 chain mRNA. Amplification of mRNA by RT-PCR, followed by direct nucleotide sequencing, revealed a homozygous C-to-T transition resulting in a premature termination codon (CGA --> TGA) on both alleles. This mutation was verified at the genomic DNA level, and both parents were shown to be heterozygous carriers of the same mutation. This is the first description of a mutation in the laminin beta 3 chain gene (LAMB3) of laminin 5 in an H-JEB patient.

Base Sequence↗

PubMed1995

A homozygous nonsense mutation in the alpha 3 chain gene of laminin 5 (LAMA3) in Herlitz junctional epidermolysis bullosa: prenatal exclusion in a fetus at risk.

Mutations in the three genes (LAMA3, LAMB3, and LAMC2) that encode the three chains (alpha 3, beta 3, and gamma 2, respectively) of laminin 5, a protein involved in epidermal-dermal adhesion, have been established as the genetic basis for the inherited blistering skin disorder, Herlitz junctional epidermolysis bullosa (H-JEB). In this study, we performed mutational analysis on genomic DNA from a child with H-JEB and identified a nonsense mutation in the alpha 3 chain gene (LAMA3) consisting of a homozygous C-to-T transition resulting in a premature termination codon (CGA-->TGA) on both alleles. The parents were shown to be heterozygous carriers of the same mutation. Direct mutation analysis was used to perform DNA-based prenatal diagnosis from a chorionic villus biopsy at 10 weeks' gestation in a subsequent pregnancy. The fetus was predicted to be genotypically normal with respect to the LAMA3 mutation.

Base Sequence↗

PubMed1995

Molecular cloning of human G alpha q cDNA and chromosomal localization of the G alpha q gene (GNAQ) and a processed pseudogene.

G alpha q is the alpha subunit of one of the heterotrimeric GTP-binding proteins that mediates stimulation of phospholipase C beta. We report the isolation and characterization of cDNA clones from a frontal cortex cDNA library encoding human G alpha q. The encoded protein is 359 amino acids long and is identical in all but one amino acid residue to mouse G alpha q. Analysis of human genomic DNA reveals an intronless sequence with strong homology to human G alpha q cDNA. In comparison to G alpha q cDNA, this genomic DNA sequence includes several small deletions and insertions that alter the reading frame, multiple single base changes, and a premature termination codon in the open reading frame, hallmarks of a processed pseudogene. Probes derived from human G alpha q cDNA sequence map to both chromosomes 2 and 9 in high-stringency genomic blot analyses of DNA from a panel of human-rodent hybrid cell lines. PCR primers that selectively amplify the pseudogene sequence generate a product only when DNA containing human chromosome 2 is used as the template, indicating that the authentic G alpha q gene (GNAQ) is located on chromosome 9. Regional localization by FISH analysis places GNAQ at 9q21 and the pseudogene at 2q14.3-q21.

Animals↗

PubMed1999

Sequence analysis of exon 8 of MAO-A gene in alcoholics with antisocial personality and normal controls.

Brunner et al. (1993, Science 262, 578-580) reported a family in which several males were affected by a syndrome of borderline mental retardation and abnormal behavior. Sequencing of exon 8 of the MAO-A gene revealed a mutation that results in a termination codon and was associated with the syndrome in the family. To determine the possible role of any mutation in exon 8 of the MAO-A gene in susceptibility to alcoholism associated with antisocial personality (ASP), we sequenced genomic DNA from 50 alcoholics and 50 normal controls. We detected only the point mutation at the position 941 (T --> G). Additional samples of alcoholics and normal controls were also screened for this mutation and the mutation in exon 14 by PCR assays. Comparison of alcoholics with ASP to normal controls for both mutation frequencies in exons 8 and 14 was positive. However, the haplotype frequency differences in the above groups were borderline significant. The most common haplotype between these mutations and a (CA)n repeat marker in the gene was F1E,C6. The frequency differences between alcoholics with ASP and normal controls for this haplotype were significant (P = 0.033). In TDT analysis, comparison of the overall haplotypes, transmitted to nontransmitted, was borderline significant. These data indicate that mutations in the MAO-A gene may play a role in the development of alcoholism associated with ASP.

Alcoholism↗

PubMed2000

Statistical analysis of the 5' untranslated region of human mRNA using "Oligo-Capped" cDNA libraries.

We constructed 34 types of human "full-length enriched" and "5'-end enriched" cDNA libraries based on the "Oligo-Capping" method. We randomly picked and sequenced 10,000 clones from these libraries. BLAST analysis showed that about 50% of the cDNAs were identical to known genes. Among them, we selected 954 species of cDNA that should represent the entire sequence from the mRNA start sites. Compared with previously reported sequences, they were on average 45 bp longer in the 5'-end. Using these cDNA data, we statistically analyzed the sequence features of the 5'UTR. The average length of the 5'UTR was 125 bp, and there was little correlation with the corresponding mRNA length (correlation coefficient = 0.26). Of the 954 species of 5'UTR, 459 contained no in-frame terminator codon, which is against the common belief. Two hundred seventy-eight species contained at least one ATG codon upstream of the initiator ATG codon. We identified 569 upstream ATGs, in total, 63% of which adequately satisfied Kozak's criteria. These findings are contrary to the typical translation initiation model, which states that translation is initiated from the "first" ATG codon.

5' Untranslated Regions↗

PubMed2002

Alternative splicing of brain-specific PTB defines a tissue-specific isoform pattern that predicts distinct functional roles.

Splicing of neural-specific exons is differentially regulated in neuronal and non-neuronal cells. The polypyrimidine tract binding protein (PTB) has been implicated as a negative regulator for exon splicing, whereas the brain-specific homolog of PTB, termed nPTB, promotes exon splicing exclusively in neurons. We have now isolated a novel mRNA splice variant of nPTB from non-neuronal cells. In contrast to the neural nPTB transcript, the expression of this novel isoform was absent from brain tissue and was generated in non-neuronal cells by alternative splicing to include five additional amino acid residues encoded by exon 9. In addition, we identified a brain-specific transcript containing a novel, alternatively spliced, internal exon 10. The exclusion of this 34-nucleotide exon 10 in non-neuronal tissues generates a premature termination codon and results in the truncation of the open reading frame. Our findings suggest that alternative splicing of nPTB has an important role in regulation of tissue-specific gene expression and thus in the functional activity of nPTB in neuronal and non-neuronal cells.

Alternative Splicing↗

PubMed1997

Novel stop mutation causing familial hypercholesterolemia in a Costa Rican family.

Combined heteroduplex single-strand conformation polymorphism (HEX-SSCP) analysis of the promoter and coding region of the low density lipoprotein receptor (LDLR) gene revealed a novel C to T mutation at nucleotide position 2056 in a Costa Rican patient with heterozygous familial hypercholesterolemia (FH). This nonsense mutation, Q665X, results in a termination codon in the epidermal growth factor (EGF) precursor homology domain of the mature LDLR.

Costa Rica↗

PubMed2002

Demonstration of altered splicing with the IVS3-1G --> a mutation of cathepsin C.

Papillon-Lefèvre syndrome is an autosomal recessive palmoplantar keratoderma caused by cathepsin C gene mutations. We present the second family segregating the IVS3-1G --> A mutation and demonstrate for the first time that altered splicing and decreased enzymatic activity occur. RNA analysis revealed two species in carriers, corresponding to wild-type and mutant transcripts, and only the mutant transcript in affected individuals. Sequencing of the mutant transcript revealed that it lacked exon 3, resulting in a frameshift and introduction of a premature termination codon.

Alternative Splicing↗