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S Volinia

Publications and source records attributed to S Volinia.

50 records · Page 3Linked to original sources
PubMed1989

The frequency of oligonucleotides in mammalian genic regions.

The large body of nucleic acid sequence data now available offers a unique opportunity for the characterization of individual oligonucleotides which may be specific to sequence functional domains. We have prepared algorithms for the study of the frequency distribution of all oligonucleotides of length 2-6 in DNA sequences. We have implemented them in the study of 634 mammalian DNA sequences spanning 1.782 Mb, and have obtained the distribution of the ratio between the observed frequency of oligonucleotides and their expected frequency based on independent nucleotide probabilities. We then studied the distribution of oligonucleotides (or k-tuples) of each length in a subset of 129 complete mammalian genes spanning 0.607 Mb. Eight distinct genomic regions, namely 5'-non-transcribed, first exon, first intron, intermediate exons, intermediate introns, last intron, last exon and 3'-non-transcribed, were considered. We observed that some oligonucleotides show a statistical behaviour and a regional distribution similar to that of known signal sequences. Moreover the frequency distribution of oligonucleotides of length 5 and 6 tends to become bimodal, indicating the existence of a population of very frequent oligonucleotides.

Algorithms↗
PubMed1989

A recurrent missense mutation (Arg----Gln) and a partial deletion in factor VIII gene causing severe haemophilia A.

The presence of gene lesions in coagulation factor VIII (FVIII) gene was investigated in 70 Italian patients severely affected by haemophilia A. cDNA probes specific for exons 14-26 of the FVIII gene were used. In two related patients a gene deletion removes exon 26, a gene lesion similar to that described previously in a British haemophiliac. In exon 24 a C to T transition in the reverse complement strand causes a missense mutation in the coding strand (CGA----CAA, 2209 Arg----Gln). The mutation is located in a very conserved FVIII homology region and severely reduces FVIII activity. By restriction analysis and hybridizations with oligonucleotide probes this gene alteration was found in two unrelated haemophiliacs and in their relatives.

Chromosome Deletion↗
PubMed1989

Partial gene deletion in a family with factor X deficiency.

The presence of gene lesions in coagulation factor X (FX, Stuart factor) was investigated in patients with FX deficiency or an FX abnormality (FX Friuli). The proposita had a heterozygous partial deletion of the FX gene with severe deficiency of FX activity and antigen. The lesion, which was inherited from her mother, removes the 3' portion of the gene coding for the catalytic domain of the factor. In this family, two differently affected FX genes are present, leading to double heterozygosity of the proposita and thus excluding consanguinity of parents. An apparently normal gene structure was observed in the other patient with FX abnormality, suggesting the presence of a small gene lesion.

Alleles↗
PubMed1988

Construction of a NotI linking library and isolation of new markers close to the Huntington's disease gene.

Linking clones contain sequences flanking recognition sites for enzymes cutting rarely in mammalian DNA. They can be used to obtain and correlate both physical and genetic mapping information over subregions of mammalian chromosomes. We have constructed and used a NotI linking clone library representing unmethylated NotI sites from HHW693 DNA, a hamster hybrid cell line containing 4p15-4pter and a fragment of 5p as its only human chromosome contribution. Human clones were identified by hybridisation with a cloned human repeat sequence, and localised further to subregions of human chromosome 4p15-4pter using a panel of additional hybrids. Clones from the region distal to the DNA probes (D4S10, D4S43, D4S95) linked to the Huntington's disease mutation, were further analysed. Four markers close to the HD gene: D4S111, D4S113, D4S114 and clone 417 are described here. In addition to serving as markers in physical and genetic mapping experiments, these linking clones provide probes next to cleavable NotI sites, and can therefore be used to screen NotI based chromosome jumping libraries. They also provide indications for potential gene sequences, identifiable as evolutionarily conserved sequences.

Chromosome Mapping↗
PubMed1988

Co-localization of rare oligonucleotides and regulatory elements in mammalian upstream gene regions.

In order to identify putative control signals of gene expression, 634 mammalian DNA sequences spanning 1.8 x 10(6) base-pairs were analysed and the frequencies of 1024 oligonucleotides five bases long (5-tuples) were determined. We defined as rare those 5-tuples having an observed frequency less than 50% of that expected by chance on the basis of base composition, and which had a reduction in frequency not attributable to CpG suppression or to coding constraints. Very few rare 5-tuples were identified; in addition, three oligonucleotides, reverse complements of rare 5-tuples, were found to have a frequency ranging between 0.582 and 0.671. The frequency of most of the rare 5-tuples was higher in 5' promoter regions as compared to exonic segments, so imitating the distribution pattern of known signals. Some of the rare 5-tuples identified by this strategy belonged to a portion of the nine base-pair binding site in promoters, which is also known as the octamer motif. In addition, three of the rare oligonucleotides were found to be located within other regulatory elements, previously identified by techniques of molecular biology. Two rare 5-tuples were found within sites of interaction between DNA and proteins, one of them being a transcriptional factor. The available data about known control sequences involved in gene expression in mammals therefore provide evidence for a role in gene regulation of the rare oligonucleotide selected.

Animals↗
PubMed1988

A HindIII RFLP and a gene lesion in the coagulation factor VIII gene.

The presence and inheritance of restriction fragment length polymorphisms (RFLPs) and gene lesions in the coagulation factor VIII gene were investigated in 15 hemophilia families. An abnormal HindIII 2.6-kb band, previously detected in a severe hemophiliac, was observed in a not severely affected patient and also in the normal gene of a woman carrying a hemophilic gene in which the lesions was found. The TaqI site in exon 24 of this defective gene was removed by a C to T transition causing an amino acid change (Arg----Gln). Very low amounts of factor VIII activity and antigen were detected in the severely affected grandson. The presence of the HindIII 2.6-kb fragment in both normal and pathological genes indicates that a factor VIII RFLP without functional meaning was found. Its frequency, determined in 60 chromosomes, is 0.18. Double digestions enabled us to map the polymorphic site 3' to the exon 19.

Antigens↗
PubMed1988

A frequent factor XII gene mutation in Hageman trait.

An additional TaqI restriction site was mapped in intron 2 of the factor XII gene. The site was found only in subjects with total or partial factor XII deficiency and thus represents the true gene lesion or a very tightly linked restriction fragment length polymorphism. The altered gene identified by this marker is present in four (three heterozygotes and one homozygote) of five unrelated Hageman trait subjects from different Italian regions. In the homozygous state the altered gene gives rise to a very marked reduction of factor XII activity. No deletion was found in the deficient factor XII genes.

Blotting, Southern↗
PubMed1988

von Willebrand disease investigated by two novel RFLPs.

Two partial cDNAs for von Willebrand factor (vWF) were used to investigate gene lesions and restriction fragment length polymorphisms (RFLPs) in vW disease (vWd) and normal controls. No gene alteration was detected but two TaqI RFLPs, likely to be intronic and originating from point mutations, were found in the 3' part of vWF gene. The two TaqI RFLPs, identified by the same probe, are informative in approximately 50% of the subjects. Used in combination with two other known RFLPs, they define several haplotypes similarly distributed in vWd and normals. Linkage disequilibrium between loci identified by the RFLPs is present. In a family study the RFLP patterns demonstrate homozygosity for the affected vWF gene in a severe (type III) patient and identify several heterozygous subjects. The RFLPs analysis has been related to the haemostatic values and multimer distribution. In two of the four unrelated patients with severe vWd examined the RFLPs study indicates double heterozygosity for the affected vWF genes.

Genetic Linkage↗
PubMed1987

Clustering of undermethylated CCGG and GCGC sequences in the 5' region of the Ha-ras-1 oncogene of human leukemic K562 cells.

The methylation state of the CCGG and GCGC sites of the Ha-ras-1 oncogene was analysed in the human leukemic K562 cell line, which was found to actively transcribe this gene. The results obtained demonstrate that the Ha-ras-1 oncogene is extensively methylated in both exonic, intronic, VTR and 3' untranslated portions, while undermethylations are present in a CG-rich island localized upstream of exon 1, near putative transcription initiation signals. Treatment of K562 cells with 5-azacytidine induces undermethylation of the Ha-ras-1 oncogene without major differences in the accumulation of Ha-ras-1 mRNA transcripts.

Base Sequence↗
PubMed1987

RFLP analysis in families with sporadic hemophilia A. Estimate of the mutation ratio in male and female gametes.

To investigate the sporadic occurrence of hemophilia A and to estimate the sex ratio of mutation rates directly, 17 families with isolated cases of the disorder were studied by RFLP analysis and by clotting assays. Three RFLPs, one intragenic and two with close linkage to hemophilia A, were used. In eight families the RFLP study excluded the carrier status of the maternal grandmothers. Since hemostatic studies showed that the eight mothers of these propositi were hemophilia carriers, the origin of the newly mutated genes was inferred from the RFLP patterns: six hemophilic genes derived from the normal maternal grandfathers and two, from maternal grandmothers. The data indicate a higher mutation rate in males than in females, as previously suggested by segregation analysis and coagulation studies. However the sex ratio indicated by the RFLP analysis is lower than previously reported and could explain previous conflicting estimates.

Female↗
PubMedDate not supplied

Microevolution in Ferrara: isonymy 1890-1990.

The distribution of surnames in the population of the town of Ferrara, as it existed in the memory banks of the Municipality Computer in June 1990, was studied by sex, age and place of birth of residents. Random isonymy was studied separately in persons born before 1901, and in persons born in the nine decades thereafter, ending with the period 1981-90. Isonymy was higher in the older age groups studied. Also other indicators of the abundance of surnames in the distribution, the common ecological indexes derived from entropy, were calculated and compared between age groups. It was found that redundancy, as isonymy, is larger in older age classes than in younger classes. Surname effective number was defined as the inverse of isonymy corrected for sample size, and it was observed that it is practically identical with Fisher's alpha. It was then possible to separate random isonymy into two components, so that for sample size N its formulation becomes Ir = 1/alpha + 1/N It was found that in Ferrara alpha increased significantly in time, indicating enrichment of surnames in the population in the century 1890-1990.

Age Factors↗
PubMedDate not supplied

Methylation pattern of the HLA-DR alpha gene in human tissues.

The CCGG and GCGC sites of the human HLA-DR alpha gene are hypermethylated in human tissues (including B-lymphocytes, T-lymphocytes, muscle, brain, sperm, skin, kidney, suprarenal and mammary glands) and three B-lymphoid cell lines. Therefore, the HLA-DR alpha gene can be transcribed even though extensively methylated. The only exception to the hypermethylated state of the HLA-DR alpha gene is represented by one or both of the two HhaI sites (H1 and H2) localized in the 5' portion of the gene. Analysis of the computer-generated secondary structure of the HLA-DR alpha mRNA suggests that the H1 and H2 sites belong to a region (5'-GAGCGCCCA-3'/5'-UGAGCGCUC-3') exhibiting extensive base pairing. Therefore, unmethylation of these CG sites can contribute in preventing mCG----TG/CA changes in this region, which would lead to extensive alterations of the secondary structure of the 5' portion of the HLA-DR alpha MRNA. On the other hand, the selective pressure to maintain unaltered the methylated CG dinucleotides in the coding regions of the HLA-DR alpha gene could be due to codon restrictions, since the majority of the methylation-related CG----TG or CG----CA variations would generate aminoacid changes. Accordingly, the analysis of different HLA-DR alpha genomic sequences indicates that variations of the CpG dinucleotides occur only in the non-coding portions of the HLA-DR alpha gene.

Base Sequence↗
PubMedDate not supplied

DNA elements target of transcriptional factors are not restricted to long terminal repeat of human immunodeficiency virus.

In this report we show that signals for transcriptional factors are not restricted to the HIV-1 LTR, but are present throughout the HIV-1 genome. Furthermore, we identified a sequence, AGAACAGATG, highly homologous to the X-box of class II MHC genes and located within the tat-IVS/env region of HIV-1. Double stranded oligonucleotides mimicking the HIV-1 region containing AGAACAGATG were synthesized and band shift experiments were performed demonstrating that this HIV-1 genomic region binds nuclear proteins. We further demonstrate that the binding of nuclear factors to this tat-IVS/env HIV-1 sequence is competed for, in the band-shift assay, by the highly homologous X-box of the promoter of the human HLA-DR alpha gene. The presence in the HIV-1 genome of DNA sequences homologous or identical to regulatory sequences of cellular genes represents a potential mechanism of predation of DNA elements recognized by DNA binding proteins.

Base Sequence↗