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D N Cooper

Publications and source records attributed to D N Cooper.

At least 37 records · Page 2Linked to original sources
PubMed2000

Identification of an intronic regulatory element in the human protein C (PROC) gene.

Regulatory DNA elements responsible for human protein C (PROC) gene expression have previously been identified in the upstream promoter region and first (untranslated) exon of the gene. Here we show that an additional sequence element located more than 500 bp downstream of the core promoter within intron 1 further enhances PROC promoter-driven reporter gene expression in human hepatoma cells. In common with core promoter constructs used in previous studies, the activity of this 3'-extended regulatory region is diminished by a naturally occurring promoter mutation. However, in contrast to constructs lacking intronic sequence, the promoter/intron regulatory region is repressed rather than activated by the transcription factor HNF-1. Using both conventional alignment procedures and complexity analysis to study the human and canine PROC sequences, we identified two conserved intronic regions, which were tested for their involvement in gene regulation. High-level gene expression from the intron-coupled promoter was dependent upon the integrity of a 142 bp sequence element, a duplicate copy of which is located in an upstream region of the PROC gene that possesses enhancer activity. These findings emphasise the potential importance of intragenic sequences for gene regulation and serve to illustrate that the results of PROC promoter/reporter gene experiments are critically dependent upon the sequence context. The identification of such intragenic elements is relevant to the analysis of human genetic disease since it will facilitate the detection and functional evaluation of regulatory mutations and polymorphisms.

Base Sequence↗
PubMed2000

Changes in primary DNA sequence complexity influence the phenotypic consequences of mutations in human gene regulatory regions.

No general rules have been proposed to account for the functional consequences of gene regulatory mutations. In a first attempt to establish the nature of such rules, an analysis was performed of the DNA sequence context of 153 different single base-pair substitutions in the regulatory regions of 65 different human genes underlying inherited disease. Use of a recently proposed measure of DNA sequence complexity (taking into account the level of structural repetitiveness of a DNA sequence, rather than simply the oligonucleotide composition) has served to demonstrate that the concomitant change in local DNA sequence complexity surrounding a substituted nucleotide is related to the likelihood of a regulatory mutation coming to clinical attention. Mutations that led to an increase in complexity exhibited higher odds ratios in favour of pathological consequences than mutations that led to a decrease or left complexity unchanged. This relationship, however, was discernible only for pyrimidine-to-purine transversions. Odds ratios for other types of substitution were not found to be significantly associated with local changes in sequence complexity, even though a trend similar to that observed for Y-->R transversions was also apparent for transitions. These findings suggest that the maintenance of a defined level of DNA sequence complexity, or at least the avoidance of an increase in sequence complexity, is a critical prerequisite for the function of gene regulatory regions.

Base Sequence↗
PubMed2000

Molecular analysis of the genotype-phenotype relationship in factor X deficiency.

Factor X deficiency is a rare haemorrhagic condition, normally inherited as an autosomal recessive trait, in which a variable clinical presentation correlates poorly with laboratory phenotype. The factor X (F10) genes of 14 unrelated individuals with factor X deficiency (12 familial and two sporadic cases) were sequenced yielding a total of 13 novel mutations. Family studies were performed in order to distinguish the contributions of individual mutant F10 alleles to the clinical and laboratory phenotypes. Missense mutations were studied by means of molecular modelling, whereas single basepair substitutions in splice sites and the 5' flanking region were examined by in vitro splicing assay and luciferase reporter gene assay respectively. The deletion allele of a novel hexanucleotide insertion/deletion polymorphism in the F10 gene promoter region was shown by reporter gene assay, to reduce promoter activity by approximately 20%. One family manifesting an autosomal dominant pattern of inheritance possessed three clinically affected members who were heterozygous for a splice-site mutation that was predicted to lead to the production of a truncated protein product. A model which accounts for the dominant negative effect of this lesion is presented. Variation in the antigen level of heterozygous relatives of probands was found to be significantly higher between families than within families, consistent with the view that the nature of the F10 lesion(s) segregating in a given family is a prime determinant of the laboratory phenotype. By contrast, no such relationship could be discerned between laboratory phenotype and polymorphism genotype.

Base Sequence↗
PubMed2000

Molecular analysis of the 5'-flanking region of the neurofibromatosis type 1 (NF1) gene: identification of five sequence variants.

Dideoxy fingerprinting was used to analyse the 5' flanking region of the neurofibromin (NF1) gene in a panel of 380 neurofibromatosis type 1 (NF1) patients. Five polymorphisms/rare variants were identified at positions -412, - 402, + 16, + 25 and + 132, but control data indicated that these were unlikely to be of pathological significance. Promoter mutations in the NF1 gene are not, therefore, a common cause of NF1. This notwithstanding, a reporter gene assay was performed to determine if these variants could affect the expression of the NF1 gene, and all three changes in the 5'-untranslated region (UTR) (+ 16, + 25, + 132) were found to be associated with a 60-70% increase in reporter gene expression.

DNA Fingerprinting↗
PubMed2000

Characterization of the interaction between galectin-1 and lymphocyte glycoproteins CD45 and Thy-1.

Galectin-1 is a sugar binding protein specific for beta-galactosides and not requiring metal ions for binding activity. It exists as a soluble protein which forms a noncovalent homodimer and is expressed with a broad tissue distribution. Recently, galectin-1 has been shown to play a possible role in the immune system mediating apoptosis of activated T cells with indirect evidence suggesting that galectin-1 interacts with the heavily glycosylated, transmembrane, protein phosphotyrosine phosphatase CD45. The interaction of galectin-1 with purified lymphocyte cell surface proteins was studied using surface plasmon resonance in a BIAcoretrade mark. Galectin-1 was shown to bind CD45 and Thy-1 in a carbohydrate-dependent manner. Several galectin-1 molecules could bind each CD45 molecule. The dissociation constant of dimeric galectin-1 binding to CD45 was measured at approximately 5 microM, indicating the concentration at which cross-linking of cell surface glycoproteins by galectin-1 would occur. A possible role for galectin-1 in the organization of cell surface glycoproteins is discussed.

Animals↗
PubMed1999

Evolution of the proximal promoter region of the mammalian growth hormone gene.

The evolutionary relationship between the proximal growth hormone (GH) gene promoter sequences of 12 mammalian species was explored by comparison of their trinucleotide composition and by multiple sequence alignment. Both approaches yielded results that were consistent with the known fossil record-based phylogeny of the analysed sequences, suggesting that the two methods of tree reconstruction might be equally efficient and reliable. The pattern of evolution inferred for the mammalian GH gene promoters was found to vary both temporally and spatially. Thus, two distinct regions devoid of any evolutionary changes exist in primates, but only one of these 'gaps' is also observed in rodents, and neither is seen in ruminants. Furthermore, different evolutionary rates must have prevailed during different periods of evolutionary time and in different lineages, with a dramatic increase in evolutionary rate apparent in primates. Since a similar pattern of discontinuity has been previously noted for the evolution of the GH-coding regions, it may reflect the action of positive selection operating upon the GH gene as a single cohesive unit. Strong evidence for the action of gene conversion between primate GH gene promoters is provided by the fact that the human GH1 and GH2 sequences, which are thought to have diverged before the divergence of Old World monkeys from great apes, are more similar to one another than either is to the rhesus monkey GH2 promoter. Finally, it was noted that a number of nucleotide positions in the GH1 gene promoter that are polymorphic in humans appear to be highly conserved in mammals. This apparent conundrum, which could represent a caveat for the interpretation of phylogenetic footprinting studies, is potentially explicable in terms either of reduced genetic diversity in highly inbred animal species or insufficient population data from non-human species.

Animals↗
PubMed1999

Disentangling the perturbational effects of amino acid substitutions in the DNA-binding domain of p53.

The spectrum of somatic cancer-associated missense mutations in the human TP53 gene was studied in order to assess the potential structural and functional importance of various intra-molecular properties associated with these substitutions. Relating the observed frequency of particular amino acid substitutions in the p53 DNA-binding domain to their expected frequency, as calculated from DNA sequence-dependent mutation rates, yielded estimates of their relative clinical observation likelihood (RCOL). Several biophysical properties were found to display significant covariation with RCOL values. Thus RCOL values were observed to decrease with increasing solvent accessibility of the substituted residue and with increasing distance from the p53 DNA-binding and Zn2+ -binding sites. The number of adverse steric interactions introduced by an amino acid replacement was found to be positively correlated with its RCOL value, irrespective of the magnitude of the interactions. A gain in hydrogen bond number was found to be only half as likely to come to clinical attention as mutations involving either a reduction or no change in hydrogen bond number. When the difference in potential energy between the wild-type and mutant DNA-binding domains was considered, RCOL values exhibited a minimum around changes of zero. Finally, classification of mutated residues in terms of their protein/solvent environment yielded, for somatic p53 mutations, RCOL values that resembled those previously determined for inherited mutations of human factor IX causing haemophilia B, suggesting that similar mechanisms may be responsible for the mutation-related perturbation of biological function in different protein folds.

Amino Acid Substitution↗
PubMed1999

Induction of differentiation and apoptosis in the prostate cancer cell line LNCaP by sodium butyrate and galectin-1.

Galectin-1 has been implicated in the process of vertebrate developmental regulation. Sodium butyrate is an established differentiation-inducing agent and has been shown to increase galectin-1 expression in colon carcinoma cells. We studied the roles of butyrate and galectin-1 in the induction of differentiation and apoptosis in the prostate cancer cell line LNCaP. Treatment of LNCaP cells with butyrate resulted in induction of galectin-1 expression in a time- and dose-dependent manner. Treatment with butyrate also resulted in inhibition of proliferation, morphologic changes consistent with a differentiated phenotype, and induction of apoptosis. Prostate specific antigen expression was transiently reduced. To determine which of these effects might be secondary to the induction of galectin-1, LNCaP cells were transfected with a galectin-1 expression vector. The transfected cells displayed growth inhibition and an increased rate of apoptosis. PSA expression was not affected. We conclude that galectin-1 may be responsible for many of the phenotypic changes resulting from butyrate treatment and may function downstream in the pathway of butyrate-induced differentiation. We also found PSA to be somewhat inconsistent as an indicator of differentiation of LNCaP cells, likely due to other factors influencing its expression.

Apoptosis↗
PubMed1999

Differential expression of endogenous galectin-1 and galectin-3 in human prostate cancer cell lines and effects of overexpressing galectin-1 on cell phenotype.

We have analyzed the expression of galectin-1 and galectin-3 in four human prostate carcinoma cell lines. Northern analysis and immunoblotting experiments showed that three cell lines express both galectins. However, only galectin-1 was detected on the surface of these cells. The LNCaP line expressed neither galectin. LNCaP was transfected with galectin-1 and four clones were isolated, all of which expressed galectin-1 on the cell surface. Kinetics of binding to extracellular matrix proteins appeared to be accelerated in the transfected lines, but overall binding was not enhanced. When the same experiments were performed in the presence of EDTA to eliminate the effects of integrins, binding of a galectin-1 clone to laminin and fibronectin was increased relative to the control cell line. We propose that galectins may contribute to the adhesive properties of some prostate cancer cells.

Antigens, Differentiation↗
PubMed1998

The human gene mutation database.

The Human Gene Mutation Database (HGMD) represents a comprehensive core collection of data on published germline mutations in nuclear genes underlying human inherited disease. By September 1997, the database contained nearly 12 000 different lesions in a total of 636 different genes, with new entries currently accumulating at a rate of over 2000 per annum. Although originally established for the scientific study of mutational mechanisms in human genes, HGMD has acquired a much broader utility to researchers, physicians and genetic counsellors so that it was made publicly available at http://uwcm.ac.uk/uwcm/mg/hgmd0.html in April 1996. Mutation data in HGMD are accessible on the basis of every gene being allocated one web page per mutation type, if data of that type are present. Meaningful integration with phenotypic, structural and mapping information has been accomplished through bi-directional links between HGMD and both the Genome Database (GDB) and Online Mendelian Inheritance in Man (OMIM), Baltimore, USA. Hypertext links have also been established to Medline abstracts through Entrez , and to a collection of 458 reference cDNA sequences also used for data checking. Being both comprehensive and fully integrated into the existing bioinformatics structures relevant to human genetics, HGMD has established itself as the central core database of inherited human gene mutations.

Computer Communication Networks↗
PubMed1998

Gross deletions of the neurofibromatosis type 1 (NF1) gene are predominantly of maternal origin and commonly associated with a learning disability, dysmorphic features and developmental delay.

Mutation screening in neurofibromatosis type 1 (NF1) families has long been hampered by the complexity of the NF1 gene. By using a novel multi-track screening strategy, 67 NF1 families (54 two-generation, 13 three-generation) with a de novo mutation in the germline of the first generation were studied with two extragenic and 11 intragenic markers. The pathological lesion was identified in 31 cases. Loss of heterozygosity (LOH) in the affected individual revealed a gross gene deletion in 15 of the two-generation families; in 12 (80%) of them, the deletion was maternally derived. Eleven patients with a gross deletion exhibited developmental delay, ten had dysmorphic features and six manifested a learning disability. No gross deletion was apparent in any of the 13 three-generation families, suggesting that such lesions are subject to more intense selection. In these families, the new mutation was of paternal origin in 11 kindreds and the underlying mutational event could be characterised in three of them.

Adolescent↗
PubMed1998

Variation of site-specific methylation patterns in the factor VIII (F8C) gene in human sperm DNA.

The methylation status of 12 CpG sites in three exons of the human factor VIII (F8C) gene was examined by bisulphite genomic sequencing of human sperm DNA from 14 European Caucasians and Asians. Different CpG sites were found to vary in their methylation status both within and between individuals. Strand differences in methylation status were also detected at certain sites, a finding that could reflect hemi-methylation. No evidence for systematic deviations in methylation status were found between the two ethnic groups. Only a limited correlation was observed between the level of methylation of specific CpG sites in sperm DNA and their mutability, a finding that is probably attributable to the pattern of methylation observed in mature spermatocytes not being representative of that of the germline.

Binding Sites↗
PubMed1998

The molecular genetics of growth hormone deficiency.

Although most cases of short stature associated with growth hormone (GH) deficiency are sporadic and idiopathic, some 5-30% have an affected first degree relative consistent with a genetic aetiology for the condition. Several different types of mutational lesion in the pituitary-expressed growth hormone (GH1) gene have been described in affected individuals. This review focuses primarily on the GH1 mutational spectrum and its unusual features, discusses potential mechanisms of mutagenesis and pathogenesis, and examines the correlation between mutant genotype and clinical phenotype. The characterization of pathological lesions in several other pituitary-expressed genes that are epistatic to GH1 (POU1F1, PROP1 and GHRHR) has identified additional causes of GH deficiency, the molecular genetics of which are also explored.

Base Sequence↗
PubMed1998

Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes.

The spectrum of single-base-pair substitutions logged in The Human Gene Mutation Database (HGMD), comprising 7,271 different lesions in the coding regions of 547 different human genes, was analyzed for nearest-neighbor effects on relative mutation rates. Owing to its retrospective nature, HGMD allows mutation rates to be estimated only in relative terms. Therefore, a novel methodology was devised in order to obtain these estimates in iterative fashion, correcting, at the same time, for the confounding effects of differential codon usage and for the fact that different types of amino acid replacement come to clinical attention with different probabilities. Over and above the hypermutability of CpG dinucleotides, reflected in transition rates five times the base mutation rate, only a subtle and locally confined influence of the surrounding DNA sequence on relative single-base-pair substitution rates was observed, which extended no farther than 2 bp from the substitution site. A disparity between the two DNA strands was evidenced by the fact that, when substitution rates were estimated conditional on the 5' and 3' flanking nucleotides, a significant rate difference emerged for 10 of 96 possible pairs of complementary substitutional events. Mutational bias, favoring substitutions toward flanking bases, a phenomenon reminiscent of misalignment mutagenesis, was apparent and exhibited both directionality and reading-frame sensitivity. No specific preponderance of repeat-sequence motifs was observed in the vicinity of nucleotide substitutions, but a moderate correlation between the relative mutability and thermodynamic stability of DNA triplets emerged, suggesting either inefficient DNA replication in regions of high stability or the transient stabilization of misaligned intermediates.

Base Pairing↗
PubMed1998

Three novel PROC gene lesions causing protein C deficiency.

Missense mutations, three of them novel (Asn210-->Val, Asn248-->Ile, Ala355-->Val), were found in the protein C (PROC) genes of 7 patients with inherited protein C deficiency associated with venous thrombosis. Comparison with the phenotypic effects of mutations in the analogous residues of factor IX causing haemophilia B and the use of molecular modelling has provided explanations as to how these lesions might alter either the structure, function or secretion of the protein C molecules encoded.

DNA Mutational Analysis↗