Evidence for translocation of DNA sequences during sea urchin embryogenesis

Eukaryotic DNA methylation

Eukaryotic genomes contain 5-methylcytosine (5mC) as a rare base.5mC arises by postsynthetic modification of cytosine and occurs, at least in animals, predominantly in the dinucleotide CpG. The base is not distributed randomly in these genomes but conforms to a pattern. This pattern varies between taxa but appears to be inherited in a semi-conservative fashion. At the level of the genome, gross changes in the level of DNA methylation have been noted. This has encouraged speculation that the modification may play a role in cellular differentiation. Tissue-specific patterns of DNA methylation, predicted by various models of differentiation, have been found for most vertebrate genes so far examined. A correlation has emerged between the undermethylation of these regions and their transcription, but this is not always the case. While data for eukaryotic viral sequences are less equivocal, studies of this kind cannot in isolation distinguish between undermethylation being a cause or a consequence of gene activity. If it were a cause, it is probable that the demethylation of specific CpG sites would be a necessary yet not a sufficient condition for transcription to occur. The introduction of artificially methylated DNA sequences into individual eukaryotic cells by microinjection or transformation may provide the means to elucidate these questions in the future. In the meantime, the study of eukaryotic DNA methylation promises to contribute much to our understanding of the regulation of gene expression in these organisms.

ADP-ribosyl transferase, rearrangement of DNA, and cell differentiation

Cell differentiation is the process by which genetic information is selectively expressed to produce cells with various morphologies and functions. The integrated changes necessary for this fundamentally important process have recently been the subject of intense study. This review will summarize data from several laboratories correlating differentiation with the activity of the enzyme ADP-ribosyl transferase and with changes in single-strand DNA breaks in various diverse eukaryotic systems. We will then discuss the implications of these observations for differentiation in general, including the possibility that rearrangement of genetic material is a widespread mechanism for controlling gene expression.

Chemical carcinogenesis -- the price for DNA - repair?

This essay examines the possibility of merging the mutation theory of cancer with the hypothesis that cancer is a change in the state of the differentiation of cells. It is suggested that during normal development DNA rearrangements occur, concerning genes which code for differentiation specific cell communication proteins. These proteins are responsible for the proper functioning of growth control in a multicellular organism. DNA-damaging agents - mutagens - induce DNA repair enzymes, some of which may catalyse illegitimate genome rearrangements, thus leading to a change of the balance between growth and differentiation. A cell with a selective advantage may arise and become the origin of a tumor.

Somaclonal variation - a novel source of variability from cell cultures for plant improvement

It is concluded from a review of the literature that plant cell culture itself generates genetic variability (somaclonal variation). Extensive examples are discussed of such variation in culture subclones and in regenerated plants (somaclones). A number of possible mechanisms for the origin of this phenomenon are considered. It is argued that this variation already is proving to be of significance for plant improvement. In particular the phenomenon may be employed to enhance the exchange required in sexual hybrids for the introgression of desirable alien genes into a crop species. It may also be used to generate variants of a commercial cultivar in high frequency without hybridizing to other genotypes.

A detailed comparison of the 5'-end of the ovalbumin gene cloned from chicken oviduct and erythrocyte DNA

We have examined homologous fragments of DNA cloned from two different tissues for changes in the dNA sequence which might be related to tissue specific gene expression. The 5' end of the chicken ovalbumin gene was cloned from oviduct or erythrocyte DNA DNA using cosmids as vectors. We have compared the two clones obtained by restriction enzyme digestions, analysis of heteroduplexes by electron microscopy or S1 nuclease digestion and by DNA sequencing. Our results show that whereas no alteration occured in the region of the gene assumed to be of importance for the control of transcription, a 4 nucleotide deletion/insertion was detected in the first intron of the ovalbumin gene.

An endonuclease isolated from Epstein-Barr virus-producing human lymphoblastoid cells

An endonuclease has been isolated from human B lymphoblastoid cells that copurifies with an exonucleolytic activity and has been shown to produce double-strand breaks and a high proportion of single-strandedness in phage lambda DNA in vitro. The data are consistent with a model in which single-strand cuts are made by the endonucleolytic activity, possibly in A+T-rich regions of the DNA, followed by creation of single-stranded regions (gaps) precessing from the site of a cut. Generation of overlapping gaps on opposite strands or of a gap opposite a nick would lead to the creation of the banding patterns that we have seen on electrophoretic gels. This endonucleolytic activity copurifies with other enzymes induced by Epstein-Barr virus that relate to the process of viral DNA replication in productively infected cells. However, a more general role is proposed for this class of eukaryotic endonuclease activities. A marked degree of single-strandedness has been found in the replicating DNAs of many eukaryotes, ad these gaps could be generated by endonucleases with associated exonucleolytic activity such as that reported here. This Epstein-Barr virus-induced nuclease activity has been shown to resemble the recBC nuclease isolated from the prokaryote Escherichia coli and also the endonuclease isolated from the eukaryote Chlamydomonas.

Sequence organization of animal nuclear DNA

Animal nuclear genomes contain DNA sequences of various degrees of repetition. These sequences are organized in highly ordered fashions; repetitive and nonrepetitive sequences either alternate in short periods, i.e., short [0.2-0.4 kilobases (kb) long] repeats are flanked by nonrepetitive sequences less than 2 kb long, or in longer periods, with repetitive and/or nonrepetitive sequences extending for several kilobases. There are two main categories of genome organization, namely those exhibiting short-period interspersion and those that do not. There are arguments for and against a regulatory role of short interspersed repetitive sequences. Besides the merely 'statistical' kinetic approach by conventional reassociation kinetics, sequence organization has been studied by restriction endonuclease mapping and nucleotide sequencing. Such studies have revealed some general features of the organization of the eukaryotic gene and its transcripts, namely possible 'promoters', 'leaders', 'introns', 'exons', 'flanking sequences', 'caps', ribosome-binding sites, and poly(A) sequences. This paper discusses how these elements of a gene might serve regulatory roles in its expression.

Conformational transitions in closed circular DNA molecules. II. Biological implications

A model of regulation of gene action based on the theory of conformational transitions in closed circular DNA molecules is proposed and discussed in connection with the mechanisms of cellular differentiation. The model predicts two main types of regulation of gene action (1) the change in the topological linking number of the DNA loops leading to the change in the amount of the DNA segments present in the transcriptionally active A-form and (2) the change of some nucleotide sequences in closed superhelical DNA loops resulting in conformational transitions of some of the other sequences in the same loop. The first type of regulation may explain the mechanism of terminal differentiation of the stem cells and the changes accompanying the malignant transformation. The second one may explain the variegated position effect of the gene and determination of the stem cells during ontogenesis.

DNA methylation in chromatin fractions of chick embryo cells

Transcriptionally active chromatin was prepared from cultured fibroblasts of chick embryos by fractionation after partial digestion with DNAase II. The degree of DNA methylation in the active chromatin fraction is twice that of inactive or unfractionated chromatin in unsynchronized cells and 4 to 5 times greater at the beginning of the S-phase in synchronized cells.

Some thoughts about genetics, differentiation, and malignancy

This article deals with three related questions: (1) whether malignancy is determined by genetic or epigenetic mechanisms; (2) whether epigenetic mechanisms, as conventionally defined, actually exist; (3) what criteria are appropriate for defining dominance or recessiveness of the malignant state in cell fusion experiments.

5-Bromodeoxyuridine inhibits sequence changes within inverted repeat DNA during embryogenesis

Previous studies on the genome of Strongylocentrotus purpuratus sea urchin have shown that changes in the nucleotide sequence of inverted repeat sequences occur during embryogenesis. The present study indicates that these sequence changes fail to occur when the embryos are raised in the presence of 5-bromodeoxyuridine. This drug is an analog of thymidine, is incorporated into the DNA during embryogenesis, and inhibits cell differentiation in these embryos.

Simian virus 40 recombinants are produced at high frequency during infection with genetically mixed oligomeric DNA

Classical approaches to analysis of mitotic recombination by use of simian virus 40 (SV40) are limited in usefulness because of low frequencies of recombination. To bypass the apparent rate-limiting step in normal SV40 recombination, oligomeric SV40 was constructed in vitro by ligation of mixtures of pairs of linear DNAs carrying genetically distinct temperature-sensitive mutations. Cultured monkey cells infected with the unfractionated ligation products yielded frequencies of nonparental recombinant progeny that were increased up to 500-fold relative to cells infected with a mixture of the untreated circular molecules. Pairwise crosses were performed with tsB4, tsB8, and tsBC11 DNAs, using unfractionated oligomers constructed from linear molecules cleaved by EcoRI or BamHI. In each cross the fraction of progeny with nonparental genotypes was roughly proportional to the physical distances between the mutant sites. These results suggest a random, rather than site-specific, conversion of oligomers to monomers. Somewhat surprisingly, nonligated mixtures of linear tsB4 and tsB8 DNAs, created by EcoRI digestion, produced a 40-t to 100-fold increase in the frequency of nonparental progeny. These results indicate that intermolecular associations must occur with fairly high efficiency between these linear molecules.