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At least 19 recordsLinked to original sources
PubMed1992

Methylation of the 5' flanking sequences of the ribosomal DNA in human cell lines and in a human-hamster hybrid cell line.

In a human lymphoblastoid cell line (Z83) in which rDNA genes on chromosome 22 are amplified but transcribed at a low level, immunocytological studies with antibodies to 5 methylcytidine provided evidence for hypermethylation of the rDNA. The extent of methylation of the 5' flanking sequences of the ribosomal DNA was examined by comparing the size of restriction fragments obtained by digestion of genomic DNA with EcoRI and HpaII or EcoRI and MspI. Southern blots indicated hypermethylation of the 5' flanking sequences of many copies of rRNA genes in these cells, but not in a control lymphoblastoid cell line without rDNA amplification. Results obtained with a somatic hybrid human-hamster cell line, in which the rRNA genes on the single human chromosome 22 are inactive, showed that only a small fraction of the CCGG sites in the 5' flanking sequences of the transcriptionally silent rRNA genes in this hybrid were methylated. Since inactive rRNA genes can show such a minimal level of methylation, it is likely that the extreme hypermethylation of the amplified rRNA genes in Z83 occurred in association with their inactivation rather than following it.

Animals↗
PubMed1992

Sequence and transcript analysis of the Nco2.5 Ogura-specific fragment correlated with cytoplasmic male sterility in Brassica cybrids.

Sequence analysis of the Ogura-specific mitochondrial DNA (mtDNA) fragment isolated previously from Brassica cybrids carrying Ogura cytoplasmic male sterility (cms) revealed a tRNA(fMet) sequence, a putative 138 amino acid open reading frame (orf138), and a 158 amino acid ORF (orf158) previously observed in mitochondrial genomes from several other plant species. Transcription mapping showed that both ORFs are present on a 1.4 kb cms-specific transcript. The orf158 sequence is also transcribed in fertile plants on a different mRNA, and thus is unlikely to be related to cms. On the other hand, fertile revertant plants lack transcripts of the orf138 sequence, whose possible role in the mechanism of Ogura cms is discussed.

Amino Acid Sequence↗
PubMed1992

Isolation of 2 novel RFLP markers and their localization at 2q35 by microdissection and subsequent enzymatic amplification.

We previously constructed a chromosome 2q-specific genomic library and isolated a number of microclones. In the present study, we first analyzed with Southern hybridization whether any of the microclones represent restriction fragment length polymorphisms (RFLPs), and then tried to map RFLP markers physically, using the recently developed chromosome microdissection/enzymatic amplification method. Of 13 clones analyzed, two were RFLP markers; a clone, pM2C83, showed a four-allele MspI RFLP, and the other, pM2C8, a two-allele RsaI RFLP. In order to assign the two polymorphic markers, two chromosomal segments, 2q32-q35 and 2q35-qter, on the chromosome 2 from a karyotypically normal person were microdissected, and the DNA from each segment was amplified with the polymerase chain reaction (PCR) using marker sequence-specific primers. With this method, both of the clones were assigned to 2q35. These two RFLP markers must be useful for linkage analysis of genetic diseases whose loci are at around 2q35.

Base Sequence↗
PubMed1992

Identification and characterization of a complex chromosomal replication origin in Schizosaccharomyces pombe.

In the budding yeast, S. cerevisiae, two-dimensional (2D) gel electrophoresis techniques permit mapping of DNA replication origins to short stretches of DNA (+/- 300 bp). In contrast, in mammalian cells and Drosophila, 2D gel techniques do not permit precise origin localization; the results have been interpreted to suggest that replication initiates in broad zones (several kbp or more). However, alternative techniques (replication timing, nascent strand polarity analysis, nascent strand size analysis) suggest that mammalian origins can be mapped to short DNA stretches, just like S. cerevisiae origins. Because the fission yeast, Schizosaccharomyces pombe, resembles higher organisms in several ways to a greater extent than does S. cerevisiae, we thought that S. pombe replication origins might prove to resemble--and thus be helpful models for--animal cell origins. An attempt to test this possibility using 2D gel techniques resulted in identification of a replication origin near the ura4 gene on chromosome III of S. pombe. The 2D gel patterns produced by this S. pombe origin indeed resemble the patterns produced by animal cell origins and show that the S. pombe origin cannot be precisely located. The data suggest an initiation zone of 3-5 kbp. Some aspects of the 2D gel patterns detected at the S. pombe origin cannot be explained by the rationale of initiation in broad zones, suggesting that future biochemical and genetic studies of this complex origin are likely to provide information useful in helping to understand the apparent conflict between the 2D gel mapping techniques and other mapping techniques at animal cell origins.

Chromosomes, Fungal↗
PubMed1992

Adenovirus DNA replication: the function of the covalently bound terminal protein.

Initiation of Adenovirus DNA replication in vitro requires the presence of three viral proteins (pTP, pol, DBP) and two cellular transcription factors, NFI and Oct-1, that stimulate replication more than 100-fold. NFI assists in binding and positioning of the DNA polymerase in the origin whereas Oct-1 changes the structure of origin DNA. Optimal templates contain, in addition to origin sequences, the covalently bound viral terminal protein (TP). This terminal protein stimulates the template activity over 20 fold compared to protein-free templates. To study the way in which TP exerts its function in vitro we devised a novel method to isolate and label a short origin containing fragment in which the TP was bound in a functional form. This fragment replicated very efficiently and could be used for studying the binding of other replication proteins. Employing alpha-chymotrypsin digestion we show that for enhancement of replication in vitro only a small part of TP is required.

Adenoviruses, Human↗
PubMed1992

Changes in chromatin structure due to hypomethylation induced with 5-azacytidine or DL-ethionine.

Changes in chromatin structure of the HRS60 family of repetitive sequences in tobacco DNA were studied after hypomethylation induced with 5-azacytidine or DL-ethionine. The TaqI site in the HRS60 units lies in nucleosomal core regions and its cleavage is enhanced in the hypomethylated chromatin. In contrast, the cleavage of the Sau3AI site located in linker DNA does not depend on the level of methylation of DNA.

Azacitidine↗
PubMed1979

Small-scale techniques for the analysis of recombinant plasmids.

Using the cloning of part of the T-DNA of pTiC58 from Agrobacterium tumefaciens as an example, techniques are described which enable recombinant plasmids to be mapped and used as hybridization probes. In all cases the starting material is a colony of cells grown on an agar plate which is then subjected to lysis by lysozyme and Triton X-100 in volumes of the order of 300 microliters thus eliminating the need for handling and centrifuging liquid cultures under restrictive containment conditions.

DNA Restriction Enzymes↗
PubMed1992

Hepatic DNA methylation in young, middle-aged, and senescent rats: the effect of mitogen-induced cell proliferation.

We have investigated the effect of a single dose of the hepatomitogen lead nitrate on the 5-methyldeoxycytidine (5-mdcyd) content and the HpaII, MspI, and HaeIII restriction patterns of hepatic DNA from young, middle-aged, and senescent rats. It was found that (i) the methylation pattern of genomic DNA changed significantly with age and (ii) the methylation patterns were differentially affected by the liver mitogen in the three cell populations here considered.

Aging↗
PubMed1992

The molecular biology of human hereditary central diabetes insipidus.

Molecular biology techniques have begun to shed light on the genetic basis of autosomal dominant central DI, but several very basic questions remain to be answered. The disorder was initially presumed to have a developmental, degenerative, or autoimmune basis based on the autopsy findings in the hypothalamus of a limited number of patients. The molecular cloning of the AVP-NP II gene and the clue from the Brattleboro rat that at least this one form of hereditary DI involved an AVP-NP II gene mutation allowed us to focus on this gene in our study of human hereditary DI. Our initial experiments did not show this gene to have a major structural alteration such as a deletion, insertion, or rearrangement, but the approach was not capable of detecting more suitable defects. The linkage studies provided substantial evidence that one particular OT-NP I haplotype was linked to the disease phenotype in each family, and thus, a mutation in the AVP/OT region of chromosome 20 is responsible for this disease. Ito et al. (1991) then identified a single base change in the AVP-NP II gene in affected members of one Japanese family. This change was not detected in unrelated, unaffected persons and thus is a good candidate for the mutation causing the disease in this family. However, there appears to be diversity in the molecular basis of autosomal dominant central DI as affected members of one of our families did not have this particular base change in either AVP-NP II allele and recently another distinct AVP-NP II gene base change has been associated with this disorder. One interesting question still to be addressed is how a mutation in the NP-II coding region of this gene prevents AVP release from the posterior pituitary in the rat or the human disease. Does the disrupted AVP-NP II coding sequence prevent normal processing of the mRNA so that it can not be properly translated into protein? Does the mutated AVP-NP II glycoprotein precursor protein interfere with normal post-translational processing to prevent release of AVP? Is an altered NP II protein not able to protect the AVP from proteolysis within the magnocellular neuron? An even more puzzling question is how a mutation in the gene encoding a hormone is inherited in an autosomal dominant pattern. The Brattleboro rat model follows the a priori expectation of autosomal recessive inheritance: the animal only exhibits a defect in hormone function if both genes encoding the hormone are defective.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1992

Characterization of the human HOX 7 cDNA and identification of polymorphic markers.

cDNA clones for a human HOX 7 gene obtained with homologous clones of Drosophila were used in human gene mapping studies. The human cDNA clone was isolated from a library constructed from human embryonic craniofacial material. The sequence of the cDNA demonstrates significant homology with mouse HOX 7. A search for RFLPs identified MboII and BstEII variants. A CA dinucleotide repeat with 5 alleles was also identified and allowed placement of HOX 7 into a defined linkage map. Evidence for linkage disequilibrium was found with markers tested. These results place the human HOX 7 gene in a defined position on 4p.

Amino Acid Sequence↗
PubMed1992

Computer-aided gene design.

A computer program, which runs on MS-DOS personal computers, is described that assists in the design of synthetic genes coding for proteins. The goal of the program is the design of a gene which (i) contains as many unique restriction sites as possible and (ii) uses a specific codon usage. The gene designed according to the criteria above is (i) suitable for 'modular mutagenesis' experiments and (ii) optimized for expression. The program 'reverse-translates' protein sequences into degenerated DNA sequences, generates a map of potential restriction sites and locates sequence positions where unique restriction sites can be accommodated. The nucleic acid sequence is then 'refined' according to a specific codon usage to remove any degeneration. Unique restriction sites, if potentially present, can be 'forced' into the degenerated nucleic acid sequence by using 'priority codes' assigned to different restriction sequences.

Amino Acid Sequence↗
PubMed1992

PCR-mediated cloning of HpaII tiny fragments from microdissected human chromosomes.

Vertebrate DNA contains a small fraction of unmethylated CpG-rich DNA sequences, many of which include the 5' end of a gene. This fraction can be detected by its cleavage to tiny fragments with the methylation-sensitive restriction enzyme HpaII. Thus, the isolation of HpaII tiny fragments (HTFs) from a specific chromosome region may be a useful approach for making an inventory of the genes contained in it. Using microdissection, we have isolated DNA from human chromosome band 8q24.1. The DNA was digested with HpaII, ligated to a ClaI-cut pUC plasmid, and amplified with Taq DNA polymerase and the standard M13/pUC forward and reverse sequencing primers. The amplification products were used to construct an HTF library, which is enriched for CpG-rich single-copy clones.

Animals↗