Single Gene Sequences Research Articles

Pea polyubiquitin genes: (I) structure and genomic organization.

Four polyubiquitin genes, PUB1, PUB2, PUB3 and PUB4, were isolated from a pea (Pisum sativum L. cv Alaska) genomic library and completely sequenced. They represent all of the four polyubiquitin genes of the ubiquitin gene family in pea. The coding regions of the genes contain five or six coding units arranged as tandem repeats. The different coding repeats of the four genes share homologies between 75 and 97%, encoding the same protein of 76 amino acids identical to those from other higher plants. The open reading frames of PUB1, PUB2 and PUB4 terminate in the additional amino acid, phenylalanine (F), and PUB3 terminates in isoleucine (I). The polyubiquitin genes all contain intron sequences ranging from 584 to 1114 bp immediately 5' to the ATG initiation codon of the first coding sequence. Of the four genes, three are associated with long AT-rich (85.4-89.4% A+T) sequences ranging from about 331 to 478 bp at their 5' or 3' ends. The PUB4 gene was found to be linked to a moderate to highly repetitive DNA at its 5' flanking sequence. The greater sequence homology between different genes than among individual repeating units of a gene suggests that the polyubiquitin genes may have arisen by gene duplication of a single gene sequence.

Detection of single copy gene sequences from single trypanosomes

Detection of single copy gene sequences from single trypanosomes

DNA methylation patterns in tumors derived from F9 cells resemble methylation at the blastula stage

We show here that the genome of F9 teratocarcinoma cells growing in culture is heavily methylated but undergoes massive demethylation in tumors derived by subcutaneous injection of the cells. This demethylation occurs primarily in single copy gene sequences. As a result imprinted genes acquire their characteristic monoallelic methylation patterns while non-imprinted genes undergo demethylation. The overall methylation pattern in the tumors resembles the pattern observed in the mouse preimplantation embryo. The F9 cells in the tumors apparently recognize imprinted genes, distinguish them from non-imprinted genes and change the methylation of both gene classes to the pattern which characterizes the embryo. These cells therefore have the potential of providing an abundant source of protein factors involved in establishing the methylation pattern during embryo development.

Isolating Fetal Cells From Maternal Blood

To review the rationale for and progress toward the goal of isolating and analyzing fetal cells circulating in maternal blood, and to explore the feasibility of this method in providing noninvasive prenatal cytogenetic diagnosis. Critical review of data published since the first report (1969) of fetal metaphases in maternal blood. Emphasis is placed on data since the demonstration by polymerase chain reaction (PCR) in 1989 and 1990 that fetal cells indeed exist in maternal blood. Clinical evaluations have not yet been conducted, but it is already clear that molecular technologies have allowed the unequivocal demonstration of fetal cells in maternal blood. Using PCR, our own group and others have demonstrated Y sequences and single gene sequences (eg, hemoglobin LeporeBoston) in maternal blood. Thus, fetal DNA sequences indeed exist in maternal blood. Among the various candidate cells, the most promising appear to be fetal nucleated red blood cells. We isolated nucleated red blood cells on the basis of flow-sorting for the transferrin receptor and glycophorin-A. Enriched samples were then subjected to fluorescence in situ hybridization with chromosome-specific probes. This approach allowed us to detect trisomy 21 and trisomy 18, work later confirmed by others. Isolating and analyzing fetal cells from maternal blood is clearly possible. Several key biologic questions remain--the optimal cells for isolation, frequency of cells in maternal blood, timing during gestation for maternal blood sampling, and the likelihood of persistence of fetal cells after delivery. Clinical evaluations planned by the National Institute of Child Health and Human Development will determine the sensitivity and specificity of this method and its precise role in prenatal cytogenetic diagnosis.

Detection of fetal cells in maternal blood

We report the detection of fetal cells in the maternal circulation by enzymatic amplification of a single copy gene sequence that was fetal-specific. Fetal HLA-A2-positive cells were sorted from maternal HLA-A2-negative cells by flow cytometry and confirmed by demonstration of a fetal-specific HLA-DR4 sequence. However, this sequence could not be detected in unenriched maternal DNA prepared at 28 and 32 weeks' gestation. The sensitivity of detection was 1 HLA-DR4-positive cell in 10(5) HLA-DR4-negative cells. We conclude that prenatal diagnosis of paternally inherited autosomal-dominant genetic defects may be possible by selective gene amplification of maternal peripheral blood. However, preliminary enrichment for fetal cells may be necessary.

Measurement of the sequence specificity of covalent DNA modification by antineoplastic agents using Taq DNA polymerase

A polymerase stop assay has been developed to determine the DNA nucleotide sequence specificity of covalent modification by antineoplastic agents using the thermostable DNA polymerase from Thermus aquaticus and synthetic labelled primers. The products of linear amplification are run on sequencing gels to reveal the sites of covalent drug binding. The method has been studied in detail for a number of agents including nitrogen mustards, platinum analogues and mitomycin C, and the sequence specificities obtained accord with those obtained by other procedures. The assay is advantageous in that it is not limited to a single type of DNA lesion (as in the piperidine cleavage assay for guanine-N7 alkylation), does not require a strand breakage step, and is more sensitive than other primer extension procedures which have only one cycle of polymerization. In particular the method has considerable potential for examining the sequence selectivity of damage and repair in single copy gene sequences in genomic DNA from cells.

PCR-aided DNasel footprinting of single copy gene sequences in permeabilized cells

PCR-aided DNasel footprinting of single copy gene sequences in permeabilized cells

Non-radioactive hybridization probes prepared using M13 phage vector and the universal sequencing primer.

Non-radioactive hybridization probes were prepared using the M13 phage vector and the universal sequencing primer. The probe sequence to be used was first cloned into the M13 vector, and the minus strand of the template DNA was then synthesized with the Klenow fragment of E. coli DNA polymerase I in the presence of the biotinylated nucleotide, biotin-11-dUTP, as a label. Resultant DNA was heavily biotinylated, and made up of the entire minus strand of the template DNA. The long tag sequence derived from the M13 vector may increase the sensitivity of the detection. The biotinylated hybrids were visualized with the streptavidin-alkaline phosphatase conjugate and chromogenic substrates. As shown by Southern hybridization, the probe prepared in this way could be used to detect less than 1 pg of target sequence and a single copy gene sequence in human genomic DNA within several hours of signal development.

Structure and expression of a newt cardio-skeletal myosin gene: Implications for the C value paradox

As part of our studies on the fate of the muscle lineage during amphibian limb regeneration, we have isolated genomic and cDNA sequences from a myosin heavy chain in the newt ( Notophthalmus viridescens). Notwithstanding the technical problems inherent in analysing the large newt genome, genomic and cDNA sequences have been isolated and subjected to analysis by restriction mapping, Northern hybridization, Southern hybridization and DNA sequencing. We believe these to be the first single copy newt gene sequences to have been subjected to this type of analysis. The newt gene sequences showed a striking difference from mammalian myosins in both the estimated sizes of the gene and its intervening sequences; these being much larger than in the mamalian models, it is speculated that this could contribute to the exceptional size of the newt genome. By contrast, the coding sequences displayed very high levels of sequence homology to mammalian myosins. In particular, the amino acid sequence of the newt myosin was found to have greatest homology with rat and human myosin isotypes having a similar cardio-skeletal muscle expression pattern. Despite a long evolutionary separation, newt and mammalian cardio-skeletal myosins have remained more similar to each other than have the human or rat cardiac forms to skeletal myosins within their own respective species.

A new sensitive non-isotopic method using sulfonated probes to detect picogram quantities of specific DNA sequences on blot hybridization.

The use of non-radioactive systems to detect target DNA or RNA displays many advantages such as safe manipulation, potential use in non-specialized scientific area and prolonged lifetime of the probes (one year or more). We here describe a method we have improved and optimized using sulfonated DNA probes for hybridization on dot and Southern blots. Sulfonation is an easy chemical modification procedure which does not require enzymatic coctail as does nick-translation. Sensitivity of this method has been particularly improved by using a new blocking solution, containing heparin, which allows easy and fast detection of picogram quantities of DNA. This method allows the use of nitrocellulose as well as nylon membranes with very low background. Equal resolution is obtained in comparative experiments involving both sulfonated and 32P-radiolabelled probes. Single copy gene sequences are readily detected in nuclear DNA. These results allow the use of this procedure for restriction fragment length polymorphism (RFLP) studies.

Structural genes adjacent to interspersed repetitive DNA sequences

The observation that repetitive and single copy sequences are interspersed in animal DNAs has suggested that repetitive sequences are adjacent to single copy structural gene sequences. To test this concept, single copy DNA sequences contiguous to interspersed repetitive sequences were prepared from sea urchin DNA by hydroxyapatite fractionation ( repeat-contiguous DNA fraction). These single copy sequences included about one third of the total nonrepetitive sequence in the genome as determined by the amounts recovered during the hydroxyapatite fractionation and by reassociation kinetics. 3H-labeled mRNA from sea urchin gastrula was prepared by puromycin release from polysomes and used in DNA-driven hybridization reactions. The kinetics of mRNA hybridization reactions with excess whole DNA were carefully measured, and the rate of hybridization was found to be 3–5 times slower than the corresponding single copy DNA driver reassociation rate. The mRNA hybridized with excess repeat-contiguous DNA with similar kinetics relative to the driver DNA. At completion 80% of that mRNA hybridizable with whole DNA (approximately 65%) had reacted with the repeat-contiguous DNA fraction (50%). This result shows that 80–100% of the mRNA molecules present in sea urchin embryos are transcribed from single copy DNA sequences adjacent to interspersed repetitive sequences in the genome.

5 S DNAs of Xenopus laevis and Xenopus mulleri: Evolution of a gene family

The 5 S DNA which contains the genes for 5 S RNA has been purified from the frog Xenopus mulleri and compared with the 5 S DNA of Xenopus laevis. Both DNAs contain highly repetitive sequences in which the gene sequence that codes for 5 S RNA alternates with a spacer sequence. The 5 S DNAs of X. laevis and X. mulleri comprise about 0.7% of the total DNA or about 24,000 and 9000 repeating sequences, respectively. The average repeat length within native X. laevis and X. mulleri 5 S DNA is about 0.5 to 0.6 and 1.2 to 1.5 × 10 6 daltons, respectively, each repeat of which contains a single gene sequence for 5 S RNA (0.08 × 10 6 daltons). The two DNAs differ in the average length of their spacers and no cross homology can be detected by heterologous hybridization of the two DNAs, except within the 5 S RNA gene regions. Despite their differences, the spacer sequences of X. laevis and X. mulleri 5 S DNA resemble each other enough to conclude that they have diverged from a common ancestral sequence. The multiple repeating sequences of 5 S DNA in each species have evolved as a family of similar, but not identical sequences. It is known that 5 S DNA is located at the ends (telomeres) of the long arms of most, if not all, X. laevis chromosomes. It is proposed that multiple gene sequences located on the ends of many chromosomes can evolve together as a family if there is extensive and unequal exchange of DNA sequences between homologous and non-homologous chromosomes at their ends.