Effect of the direction of DNA replication on mutagenesis by N-methyl-N''-nitro-N-nitrosoguanidine in adapted cells of Escherichia coli

Summary The methylating agent N-methyl-N-nitro-N-nitrosoguanidine preferentially induces G:C to A:T transitions at DNA base pairs with the G in one particular strand of the cI gene in a lambda prophage, in this case the non-transcribed straind, in Escherichia coli cells in which the adaptive response is induced. The same preference is found for the cI gene inserted in the genome in the inverse orientation, so the differential effect is not caused by the direction of motion of the DNA replicating fork.     

Initiation of DNA replication in higher eukaryotes

In this review, of problems concerning initiation of DNA replication in higher eukaryotes is discussed, with special emphasis on the methods of replication origin mapping and biological tests for the activity of DNA replication origins in higher eukaryotes. Protein factors interacting with replication origins are considered in detail. The main events of replication initiation in higher eukaryotes are briefly analyzed. New data on the control of replication timing of large genomic regions are discussed.     

DNA replication initiates at multiple sites on plasmid DNA in Xenopus egg extracts.

Cell-free extracts of Xenopus eggs will replicate plasmid DNA molecules under normal cell cycle control. We have used the neutral/neutral 2-D gel technique to map the sites at which DNA replication initiates in this system. Three different plasmids were studied: one containing the Xenopus rDNA repeat, one containing single copy Xenopus genomic DNA, and another containing the yeast 2 microns replication origin. 2-D gel profiles show that many potential sites of initiation are present on each plasmid, and are randomly situated at the level of resolution of this technique (500-1000 bp). Despite the abundance of sites capable of supporting the initiation of replication, pulse-chase experiments suggest that only a single randomly situated initiation event occurs on each DNA molecule. Once initiation has taken place, conventional replication forks appear to move away from this site at a rate of about 10nt/second, similar to the rate observed in vivo.     

The initiation of chromosomal DNA replication in eukaryotes

Eukaryotic DNA replication initiates at many sites on each chromosome during the S phase of the cell cycle. Each origin of replication lies in a unique chromosomal environment and can be regulated in different cell types both at the level of utilization and the time of initiation during S phase. In this review, we examine the control and the mechanism of eukaryotic origin function.     

DNA replication of histone gene repeats in Drosophila melanogaster tissue culture cells: multiple initiation sites and replication pause sites.

We showed previously that DNA replication initiates at multiple sites in the 5-kb histone gene repeating unit in early embryos of Drosophila melanogaster. The present report shows evidence that replication in the same chromosomal region initiates at multiple sites in tissue culture cells as well. First, we analyzed replication intermediates by the two-dimensional gel electrophoretic replicon mapping method and detected bubble-form replication intermediates for all fragments restricted at different sites in the repeating unit. Second, we analyzed bromodeoxyuridine-labeled nascent strands amplified by the polymerase chain reaction method and detected little differences in the size distribution of nascent strands specific to six short segments located at different sites in the repeating unit. These results strongly suggest that DNA replication initiates at multiple sites located within the repeating unit. We also found several replication pause sites located at 5' upstream regions of some histone genes.     

DNA polymerases at the replication fork in eukaryotes

The Kunkel laboratory has recently assigned polymerase (Pol) epsilon as the leading strand polymerase. In a recent issue of Molecular Cell, they now assign Pol delta as the lagging strand polymerase.     

Mechanisms and regulation of DNA replication initiation in eukaryotes

Cellular DNA replication is initiated through the action of multiprotein complexes that recognize replication start sites in the chromosome (termed origins) and facilitate duplex DNA melting within these regions. In a typical cell cycle, initiation occurs only once per origin and each round of replication is tightly coupled to cell division. To avoid aberrant origin firing and re-replication, eukaryotes tightly regulate two events in the initiation process: loading of the replicative helicase, MCM2-7, onto chromatin by the origin recognition complex (ORC), and subsequent activation of the helicase by its incorporation into a complex known as the CMG. Recent work has begun to reveal the details of an orchestrated and sequential exchange of initiation factors on DNA that give rise to a replication-competent complex, the replisome. Here, we review the molecular mechanisms that underpin eukaryotic DNA replication initiation – from selecting replication start sites to replicative helicase loading and activation – and describe how these events are often distinctly regulated across different eukaryotic model organisms.     

DNA replication initiates non-randomly at multiple sites near the c-myc gene in HeLa cells.

The origin of replication of the c-myc gene in HeLa cells was previously identified at low resolution within 3.5 kb 5' to the P1 promoter, based on replication fork polarity and the location of DNA nascent strands. To define the initiation events in the c-myc origin at higher resolution the template bias of nascent DNAs in a 12 kb c-myc domain has been analyzed by hybridization to strand specific probes. Strong switches in the asymmetry of nascent strand template preference confirm that replication initiates non-randomly at multiple sites within 2.4 kb 5' to the c-myc P1 promoter, and at other sites over a region of 12 kb or more. The strongest template biases occur in the 2.4 kb region 5' of the P1 promoter, shown earlier to contain sequences which allow the autonomous semiconservative replication of c-myc plasmids. An asymmetric pyrimidine heptanucleotide consensus sequence has been identified which occurs 12 times in the c-myc origin zone, and whose polarity exactly correlates with the polarity of nascent strand synthesis.     

Mapping structurally perturbed sites in DNA by replication arrest and run-off replication

We describe a technique for rapid fine mapping of sites of torsion-induced perturbations of DNA structure. The technique involves strand scission or chemical base modification at structurally perturbed sites, replication arrest in a double-strand DNA sequencing reaction, and size analysis of replication products by electrophoresis on sequencing gels. Besides being less complicated and faster than site identification by conventional end-labeling methods, the technique assures high sequence specificity through the use of oligomeric sequencing primers. This property should be useful for in vivo mapping of DNA structural perturbations with known sequence within complex genomes.     

Telomere replication and fusion in eukaryotes.

The requirement for special mechanisms to replicate the ends of linear DNA has resulted in a new model of telomere replication that includes fused telomeres as intermediates. The model suggests a mechanism for Robertsonian fusions and fissions and predicts the formation of dicentric chromosomes during certain types of cellular dysfunction. One possible molecular mechanism for covalently joining the ends of DNA before replication and reforming the ends afterwards is presented. Molecular and cytological evidence is cited in support of the model. The model assigns a role to membrane binding and clustering of telomeres in higher eukaryotes and explains the paired chromosome chains observed during fungal mitosis.     

Visualizing DNA replication sites in the cell nucleus.

Studies of DNA replication associated with the nuclear matrix have led to a radically new view of replication at the macroscopic level. It is proposed that individual replicons and their associated replicational assemblies (replisomes) are clustered together during active replication by attachment to the nuclear matrix at special sites termed 'clustersomes'. Direct visualization of replication sites in permeabilized cells by fluorescence microscopy following biotin-11-dUTP incorporation provides support for this model. Discrete replication granules are observed with sizes and numbers consistent with each granule being a site of replicon cluster synthesis. Distinct patterns of these sites are seen in different periods of S-phase. Both the individual granules and their early and late S-phase dependent patterns are strikingly maintained following extraction of the cells for in situ nuclear matrix structures. Similar results were obtained when probing in vivo sites of replication following incorporation of 5-bromodeoxyuridine. The three-dimensional organization of these replicational granules (clustersomes) is studied using confocal light microscopy and an appropriate multidimensional image analysis system.