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At least 865 records · Page 48Linked to original sources
PubMed2000

Variations of the bilirubin uridine-diphosphoglucuronosyl transferase 1A1 gene in healthy Taiwanese.

The activity of uridine-diphosphoglucuronosyl transferase 1 (UGT1) may influence the concentration of serum bilirubin. Because UGT1 is too labile to be measured with classical biochemical methods, we analysed the whole UGT1A1 gene in 290 healthy Taiwanese adults by using the polymerase chain reaction method, and investigated the relationship between UGT1A1 genotypes and serum bilirubin levels. The results showed that slightly more than 50% of the subjects had one or more variant sites in UGT1A1 gene. The most common variant was A(TA)6TAA/A(TA)7TAA (6/7) in the promoter area, followed by heterozygous variation within the coding region, compound heterozygous and homozygous variations. Among the four variant sites within the coding region, 211 G to A was the predominate one, 1091 C to T was a novel variation, and 686 C to A was associated with 6/7. Subjects with 6/7 or heterozygous variation within the coding region or compound heterozygous (plus one homozygous) variation had significantly higher bilirubin levels than those with wild UGT1A1 gene. When the 290 subjects were stratified into six groups according to their serum bilirubin concentrations, the bilirubin levels were correlated well to the frequencies of variant UGT1A1 gene. Our results show that there is a strong association between UGT1A1 gene and bilirubin levels in healthy Taiwanese adults. The occurrence of A(TA)7TAA allele was relatively rare and the variation rate within the coding region was much higher in Taiwanese compared to that in Caucasians.

Adult↗
PubMed1999

Flip and flop variants of AMPA receptor subunits in the human cerebellum: implication for the selective vulnerability of Purkinje cells.

We investigated the distribution of messenger RNAs coding for flip and flop splice variants ofAMPA receptor subunits in the human cerebellum to determine the relevance of AMPA receptors in the selective vulnerability of Purkinje cells to ischemia. Purkinje cells more abundantly expressed transcripts for flip variant of GluR-A, GluR-C, and GluR-D than granule cells, whereas transcripts for flop variants and GluR-B flip were expressed at similar levels on Purkinje cells and granule cells. These results suggest that human Purkinje cells possess AMPA receptors of the slowly desensitizing class as compared to granule cells. This differential distribution may explain the selective vulnerability of Purkinje cells.

Cell Death↗
PubMed1991

Tissue-specific and dexamethasone-inducible expression of alkaline phosphatase from alternative promoters of the rat bone/liver/kidney/placenta gene.

The rat Bone/Liver/kidney/Placenta Alkaline Phosphatase (ALP) is transcribed from two alternative promoters spaced over 25 kb apart, resulting in two variant transcripts that are identical in their coding sequence. We investigated the steady-state levels of the two variant transcripts in various rat tissues and cell lines using the polymerase chain reaction (PCR) amplification for RNA phenotyping, RNase protection, and northern blot analysis. Our results demonstrate that ALP transcripts from the upstream promoter are preferentially expressed in calvariae, and are almost exclusively expressed in ROS17/2.8 osteogenic sarcoma cells. In contrast, the downstream promoter is preferentially expressed in kidney. Moreover, the increase in ALP activity and mRNA levels following dexamethasone treatment of ROS17/2.8 cells is correlated with an increase in the level of transcripts from the upstream promoter. Thus, the two alternative promoters of the rat BLKP ALP gene are involved in cell-specific and dexamethasone-inducible regulation of its expression.

Alkaline Phosphatase↗
PubMed2000

The human peroxisome proliferator-activated receptor alpha gene: identification and functional characterization of two natural allelic variants.

Peroxisome proliferator-activated receptor (PPAR)alpha-null mice have a defect in fatty acid metabolism but reproduce normally. The lack of a detrimental effect of the null phenotype in development and reproduction opens up the possibility for null or variant PPARalpha gene (PPARA) alleles in humans. To search the coding region and splice junctions for mutant and variant PPARalpha alleles, the human PPARalpha gene was cloned and characterized, and sequencing by polymerase chain reaction was carried out. Two point mutations in the human gene were found in the DNA binding domain at codons for amino acids 131 and 162. The allele containing the mutation in codon 162 (CTT to GTT, L162V) designated PPARA*3, was found at a high frequency in a Northern Indian population. Transfection assays of this mutant showed that the non-ligand dependent transactivation activity was less than one-half as active as the wild-type receptor. PPARA*3 was also unresponsive to low concentrations of ligand as compared to the wild-type PPARA*1 receptor. However, the difference is ligand concentration-dependent; at concentrations of the peroxisome proliferator Wy-14 643 > 25 microM, induction activity was restored in this variant's transactivation activity to a level five-fold greater as compared with wild-type PPARA*1 with no ligand. The mutation in codon 131 (CGA to CAA, R131Q), designated PPARA*2 is less frequent than PPARA*3, and the constitutive ligand independent activity was slightly higher than PPARA*1. Increasing concentrations of Wy-14 643 activated PPARA*2 similar to that observed with PPARA*1. The biological significance of these novel PPARalpha alleles remains to be established. It will be of great interest to determine whether these alleles are associated with differential response to fibrate therapy.

Alleles↗
PubMed2006

MSX1 and orofacial clefting with and without tooth agenesis.

MSX1 has been considered a strong candidate for orofacial clefting, based on mouse expression studies and knockout models, as well as association and linkage studies in humans. MSX1 mutations are also causal for hereditary tooth agenesis. We tested the hypothesis that individuals with orofacial clefting with or without tooth agenesis have MSX1 coding mutations by screening 33 individuals with cleft lip with or without cleft palate (CL/P) and 19 individuals with both orofacial clefting and tooth agenesis. Although no MSX1 coding mutations were identified, the known 101C > G variant occurred more often in subjects with both CL/P and tooth agenesis (p = 0.0008), while the *6C-T variant was found more often in CL/P subjects (p = 0.001). Coding mutations in MSX1 are not the cause of orofacial clefting with or without tooth agenesis in this study population. However, the significant association of MSX1 with both phenotypes implies that MSX1 regulatory elements may be mutated.

Adolescent↗
PubMed2003

Alzheimer disease-associated cystatin C variant undergoes impaired secretion.

CST3 is the coding gene for cystatin C (CysC). CST3 B/B homozygosity is associated with an increased risk of developing Alzheimer disease. We performed CysC analysis on human primary skin fibroblasts obtained from donors carrying A/A, A/B, and B/B CST3. Pulse-chase experiments demonstrated that the release of the B variant of CysC has a different temporal pattern compared to that of the A one. Fibroblasts B/B homozygous displayed a reduced secretion of CysC due to a less efficient cleavage of the signal peptide, as suggested by high-resolution Western blot analysis and by in vitro assay. In the brain, the reduced level of CysC may represent the molecular factor responsible for the increased risk of Alzheimer disease.

Aged↗
PubMed2000

Patterns of variant polyadenylation signal usage in human genes.

The formation of mature mRNAs in vertebrates involves the cleavage and polyadenylation of the pre-mRNA, 10-30 nt downstream of an AAUAAA or AUUAAA signal sequence. The extensive cDNA data now available shows that these hexamers are not strictly conserved. In order to identify variant polyadenylation signals on a large scale, we compared over 8700 human 3' untranslated sequences to 157,775 polyadenylated expressed sequence tags (ESTs), used as markers of actual mRNA 3' ends. About 5600 EST-supported putative mRNA 3' ends were collected and analyzed for significant hexameric sequences. Known polyadenylation signals were found in only 73% of the 3' fragments. Ten single-base variants of the AAUAAA sequence were identified with a highly significant occurrence rate, potentially representing 14.9% of the actual polyadenylation signals. Of the mRNAs, 28.6% displayed two or more polyadenylation sites. In these mRNAs, the poly(A) sites proximal to the coding sequence tend to use variant signals more often, while the 3'-most site tends to use a canonical signal. The average number of ESTs associated with each signal type suggests that variant signals (including the common AUUAAA) are processed less efficiently than the canonical signal and could therefore be selected for regulatory purposes. However, the position of the site in the untranslated region may also play a role in polyadenylation rate.

3' Untranslated Regions↗
PubMed1999

Global sequence diversity of BRCA2: analysis of 71 breast cancer families and 95 control individuals of worldwide populations.

The aim of this study was to evaluate the prevalence of simple sequence variation in the BRCA2 gene. To this end, 71 breast and breast-ovarian cancer (HBC/HBOC) families along with 95 control individuals from a wide range of ethnicities were analyzed by means of denaturing high-performance liquid chromatography (DHPLC) and direct sequence analysis. In the coding (10 257 bp) and non-coding (2799 bp) sequences of BRCA2, 82 sequence variants were identified. Three different, apparently disease-associated BRCA2 mutations were found in six HBC/HBOC families (8%): two splice site mutations in introns 5 and 21, and one frameshift mutation in exon 11. In the coding region, 53 simple sequence variants were found: 35 missense mutations, one 2 bp deletion (CT) resulting in a stop at codon 3364, one nonsense mutation with a stop at codon 3326, one deletion of a complete codon (AAA) resulting in the loss of leucine, and 15 silent mutations. In the non-coding region, 26 polymorphisms were detected. Of the 79 sequence variants that were not obviously disease-associated, eight were detected only in HBC/HBOC families. The remaining 71 variants were identified in both HBC/HBOC families and control individuals. Sixty three sequence variants (80%) were specific for a continent. Forty two percent (33 out of 79) of the sequence variants were detected exclusively in Africa, though only 13% of the 332 chromosomes screened were of African origin. Our data indicate that, in BRCA2, simple sequence variation is frequent [in the coding region 1 in 194 bp (straight theta = 2.2 x 10(-4)), and in the non-coding region 1 in 108 bp (straight theta = 4.4 x 10(-4)), respectively].

Africa↗
PubMed1995

Cloning and characterisation of two new cDNAs encoding murine triple LIM domains.

We have cloned and sequenced two new cDNAs that code for proteins carrying the related triple LIM domains (acronym of Lin-11, Isl-1, Mec-3) proteins. These LIM domains show good agreement to the LIM domain consensus sequence, but also exhibit some novel variations. The 1.36-and 2.8-kb cDNAs are probably splice variants of one gene and code for 42- and 50-kDa proteins, respectively. The larger transcript has a 900-nucleotide (nt) 3' untranslated region (UTR). High levels of the 2.8-kb transcript can be detected in many tissues, and all tissues show some level of expression of both transcripts, the larger transcript being more abundant. In adult testis there are very high levels of the 1.36-kb transcript and moderate levels of the 2.8-kb transcript. The wide tissue distribution and high levels of expression suggest an important role for these proteins in cellular function.

Amino Acid Sequence↗
PubMed1992

Molecular and structural basis of hemagglutination in mengovirus.

The molecular and structural basis of mengovirus hemagglutination (HA) was investigated by the comparison of nucleotide sequences of the entire capsid coding regions of an HA+ variant, two HA- mutants, 205 and 280, and two HA+ revertants of 205. The mutants were selected after acridine mutagenesis of mengovirus-37A, a heat-stable and HA+ variant that is neurotropic in mice. HA+ revertants of mutant 205 were isolated from brain tissue of mice inoculated with mutant 205. The nucleotide sequences were determined by consensus RNA sequencing using genomic RNA templates from purified virions. Two nucleotide differences were observed in the VP1 coding region of the RNA genomes of mutants 205 and 280 in comparison to the RNA sequences of 37A and the revertants. Interpretation of these data predict substitutions of two consecutive amino acids at residues 1231 (K to R) and 1232 (P to S) of VP1 which form part of the H-I loop of VP1 found at the icosahedral fivefold axis. Analysis of the amino acid substitutions in the context of the three-dimensional structure of the mengovirus-M capsid indicated that hemagglutination most likely involves residues found at the icosahedral fivefold axis and probably does not involve the residues that form the putative cellular receptor binding site (the "pit"). Eleven amino acid differences were observed between the structural proteins of mengovirus-M and 37A, five in VP1, three in VP2, and three in VP3.

Amino Acid Sequence↗
PubMed2001

Functional analysis of human MLH1 and MSH2 missense variants and hybrid human-yeast MLH1 proteins in Saccharomyces cerevisiae.

Hereditary non-polyposis colorectal cancer (HNPCC) is an autosomal dominant inherited disease caused by defects in the process of DNA mismatch repair (MMR), and mutations in the hMLH1 or hMSH2 genes are responsible for the majority of HNPCC. In addition to clear loss-of-function mutations conferred by nonsense or frameshift alterations in the coding sequence or by splice variants, genetic screening has revealed a large number of missense codons with less obvious functional consequences. The ability to discriminate between a loss-of-function mutation and a silent polymorphism is important for genetic testing for inherited diseases like HNPCC where the opportunity exists for early diagnosis and preventive intervention. In this study, quantitative in vivo DNA MMR assays in the yeast Saccharomyces cerevisiae were performed to determine the functional significance of amino acid replacements observed in the human population. Missense codons previously observed in human genes were introduced at the homologous residue in the yeast MLH1 or MSH2 genes. This study also demonstrated feasibility of constructing genes that encode functional hybrid human-yeast MLH1 proteins. Three classes of missense codons were found: (i) complete loss of function, i.e. mutations; (ii) variants indistinguishable from wild-type protein, i.e. silent polymorphisms; and (iii) functional variants which support MMR at reduced efficiency, i.e. efficiency polymorphisms. There was a good correlation between the functional results in yeast and available human clinical data regarding penetrance of the missense codon. The results reported here raise the intriguing possibility that differences in the efficiency of DNA MMR exist between individuals in the human population due to common polymorphisms.

Adaptor Proteins, Signal Transducing↗
PubMed2004

DNA sequence analysis of monoamine oxidase B gene coding and promoter regions in Parkinson's disease cases and unrelated controls.

The allele G of the intron 13 G/A polymorphism of the monoamine oxidase B gene (MAO-B) has been associated with Parkinson's disease (PD) in several studies. Apart from a potential direct effect on splicing processes, the association of this intronic polymorphism with PD is due possibly to linkage disequilibrium with other mutations in the coding or promoter regions of the gene. We addressed this latter hypothesis by determining the DNA sequence of the entire MAO-B coding region comprising 15 exons and partial intronic sequences flanking each exon, in 33 cases with idiopathic PD and 38 unrelated controls. The promoter region of MAO-B gene up to base -1,369 from ATG (start point of mRNA translation) was also sequenced to identify variants with potential functional effects on gene transcription. In the promoter region, a new polymorphism consisting of a C to T single base change was detected in position -1,114 from ATG, with an allelic frequency of 3.5%, but it was not associated with PD risk. No commonly occurring (>10%) polymorphisms were found in the exons or the intronic sequences flanking the exons, although several rare variants were detected in the coding and promoter regions.

Aged↗
PubMed2004

Selective expansion of the newly evolved genomic variants of retrotransposon 1731 in the Drosophila genomes.

The structural variants of the regulatory and coding regions of the LTR-retrotransposon 1731 are described. Two classes of genomic copies of retrotransposon 1731, with and without frameshifting strategy to express Gag and Pol proteins, were earlier revealed in the D. melanogaster genome. Copies without frameshifting are shown to be evolved from an ancient variant with frameshifting and are widespread in the genomes of the melanogaster complex species. Position of a rare codon responsible for ribosome pausing and efficient frameshifting is identified. Two structural variants of 1731 LTRs were detected in the melanogaster complex species: the predominant structural variant A1A2 of 1731 LTR in the D. melanogaster, D. simulans, and D. sechellia genomes contains duplicated and diverged copies of 28 bp in the U3 region, whereas A1 variant lacking this duplication is expanded in the D. mauritiana genome. Selective expansion of the A1A2 variant was detected in the independently established D. melanogaster cell cultures. A1A2 variant is expressed in embryos, cell culture, and testes, whereas A1 is expressed only in testes of D. melanogaster. Relief of expression of the A1A2 but not A1 variant in the ovaries as a result of mutation in the RNA interference (RNAi) spn-E gene is shown. Thus, expansion of the recently evolved genomic variants of the LTR retrotransposon 1731 possessing a new translation strategy, duplication in the U3 region, and extended profile of expression is revealed.

Animals↗
PubMed2006

A functional variant of the dopamine D3 receptor is associated with risk and age-at-onset of essential tremor.

Familial essential tremor (ET), the most common inherited movement disorder, is generally transmitted as an autosomal dominant trait. A genome-wide scan for ET revealed one major locus on chromosome 3q13. Here, we report that the Ser9Gly variant in the dopamine D(3) receptor gene (DRD3), localized on 3q13.3, is associated and cosegregates with familial ET in 23 out of 30 French families. Sequencing revealed no other nonsynonymous variants in the DRD3-coding sequence and in the first 871 bp of the 5' flanking region. Moreover, Gly-9 homozygous patients presented with more severe and/or earlier onset forms of the disease than heterozygotes. A replication study comparing 276 patients with ET and 184 normal controls confirmed the association of the Gly-9 variant with risk and age-at-onset of ET. In human embryonic kidney (HEK) 293-transfected cells, the Gly-9 variant did not differ from the Ser-9 variant with respect to glycosylation and to anterograde and retrograde trafficking, but dopamine had an affinity that was four to five times higher. With the Gly-9 variant, the dopamine-mediated cAMP response was increased, and the mitogen-associated protein kinase (MAPK) signal was prolonged, as compared with the Ser-9 variant. The gain-of-function produced by the Gly-9 variant may explain why drugs active against tremor in Parkinson's disease (PD) are usually not effective in the treatment of ET and suggests that DRD3 partial agonists or antagonists should be considered as novel therapeutic options for patients with ET.

Adolescent↗
PubMed1985

Adenovirus early region 4 encodes functions required for efficient DNA replication, late gene expression, and host cell shutoff.

To delineate the function of adenovirus early region 4 (E4) gene products, we constructed a set of mutant viruses which carry defined lesions within this coding region. Deletion and insertion mutations within six of seven known E4 coding regions had no measurable effect on virus growth in cultured cells. A variant carrying a deletion within the last coding region (encoding a 34,000-molecular-weight polypeptide) was modestly defective, and a mutant lacking the majority of the E4 region was severely defective for growth. The phenotypes of the two defective mutants are similar and complex. Both display perturbations in DNA replication, translation of the E2A mRNA, accumulation of late viral mRNAs, and host cell shutoff.

Adenoviruses, Human↗
PubMed2003

Allelic variants in the MYOC/TIGR gene in patients with primary open-angle, exfoliative glaucoma and unaffected controls.

One of the leading causes of blindness in the world is glaucoma. The most common form is primary open-angle glaucoma (POAG). The only gene identified so far as being associated with POAG is the MYOC gene; 2-4% of the patients have been reported to carry mutations in this gene. Exfoliative glaucoma is a secondary glaucoma, in which one of the symptoms is exfoliations on the lens capsule and anterior segment of the eye. No gene has been identified as being associated with this variant. The aim of the present study was to analyze Swedish patient material for allelic variants and mutations in the coding region of the MYOC gene. Two hundred patients with POAG and 200 with exfoliative glaucoma were analyzed using enzymatic cleavage assay and denaturing high-performance liquid chromatography (dHPLC). An age-matched control group (n = 200), in whom glaucoma had been excluded, was also analyzed using dHPLC. Eight allele variants were identified, two of which were determined to be disease-causing mutations. These two disease-causing mutations were only found in POAG patients, indicating a prevalence of 1% in this patient group. This frequency is lower than that reported in other studies of other populations. No disease-causing mutations were found in the exfoliative glaucoma patients, indicating a fundamentally different genetic basis for that glaucoma variant.

Aged↗
PubMedDate not supplied

Variants of the myocilin gene in Japanese patients with normal-tension glaucoma.

Myocilin (MYOC) mutations are associated with juvenile- and adult-onset primary open-angle glaucoma (POAG). The purpose of this study was to determine whether MYOC gene mutations are associated with normal-tension glaucoma (NTG). The prevalence of MYOC mutations was determined in 80 Japanese NTG patients and 100 control subjects. In addition, the expression of mutant MYOC was determined by transforming COS-1 cells with five myocilin variants (R158Q, D208E, I360N, A363T, and I477S) and examining whether myocilin was present in the cultured cells and/or the culture medium by western blotting. Six different nucleotide sequence variants, R46Stop, R76K, R158Q, D208E, A488A, and one in the 3' non-coding region, were identified in 80 NTG patients. Variants in codon 46 (R46Stop), codon 158 (R158Q), and codon 488 (A488A) were not found in the 100 normal controls. The frequency of other sequence changes (R76K, D208E, and 3' non-coding) in NTG patients did not differ significantly from the frequencies in the control subjects. COS-1 cells transfected with the wild type, R158Q, or D208E variants secreted myocilin into the culture medium. On the other hand, the detected myocilin was significantly reduced in the medium of cells transfected with the I360N, A363T, or I477S variants that were previously identified as mutations for POAG. Definitive evidence of MYOC variants associated with NTG was not found.

Animals↗
PubMed2003

EP2 splicing variants in rhesus monkey (Macaca mulatta) epididymis.

The expression pattern of EP2 variants was examined in the rhesus monkey (Macaca mulatta). Using reverse transcriptase-polymerase chain reaction and rapid amplification of complementary cDNA protocols, 11 message variants were identified in rhesus epididymis, only three of which (EP2B, EP2C, and EP2E) have previously been reported. The most abundant variant found in human, EP2A, was not found in rhesus. Seven of the eight new rhesus EP2 variants (EP2J-EP2Q) use previously unidentified 5'-splicing sites in exon 3, and four variants use three previously unidentified exons whose counterparts are present in the human EP2 gene. Overall, 3 of the 11 variants, EP2C, EP2E, and EP2Q, code for beta-defensin-like peptides whose probable physiological role is to protect the male reproductive tract against microbial invasions. Because of the complex splicing pattern that causes some downstream exons to be read in any of the three reading frames, the N-termini of the other eight EP2 peptide variants consist of a partial beta-defensin motif with three cysteines, followed by amino acid sequences that have no recognizable homology to known proteins.

Alternative Splicing↗