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.     

Mechanism and regulation of DNA end resection in eukaryotes

The repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) is initiated by nucleolytic degradation of the 5′-terminated strands in a process termed end resection. End resection generates 3′-single-stranded DNA tails, substrates for Rad51 to catalyze homologous pairing and DNA strand exchange, and for activation of the DNA damage checkpoint. The commonly accepted view is that end resection occurs by a two-step mechanism. In the first step, Sae2/CtIP activates the Mre11–Rad50–Xrs2/Nbs1 (MRX/N) complex to endonucleolytically cleave the 5′-terminated DNA strands close to break ends, and in the second step Exo1 and/or Dna2 nucleases extend the resected tracts to produce long 3′-ssDNA-tailed intermediates. Initiation of resection commits a cell to repair a DSB by HR because long ssDNA overhangs are poor substrates for non-homologous end joining (NHEJ). Thus, the initiation of end resection has emerged as a critical control point for repair pathway choice. Here, I review recent studies on the mechanism of end resection and how this process is regulated to ensure the most appropriate repair outcome.     

The topology of circular DNA]

A non-orientable structure, said M?bius stripe, is proposed for certain types of circular DNA. This structure could account for particular forms, such as dimers, double length molecules, or catenans which are molecules topologically interwomen. On the other hand, it is suggested that a second structure derived from the same principal of non-orientability could have gendered the dynamics of DNA replication at the origin of life: this is hypothesis of archetype M?bius strip.     

Single-stranded DNA from viruses, prokaryotes and eukaryotes]

The review presents the results of investigations of single-stranded DNAs of viruses, bacteria and cells of higher organisms. Methods of revealing, isolating and analysis of these DNAs are presented. A large variety of single-stranded DNA containing genomes of plant and animal viruses was revealed. Attention is drawn to the integration and replication of viral genomes. Results of SV40 integration during the first two days after infection of Chinese hamster cells are shown. Results of studying multi-copy single-stranded DNA in bacterial cells were analysed. In separate sections, the replication of plasmid single-stranded DNA was studied as well as the problem of plasmid stability in cells. Advances in bacteria transformation studies are stated. Data of single-stranded DNA investigation in cells of higher organisms are mainly presented on the example of early embryos. Data on the analysis of gene hypersensitivity to nuclease S1 are given. A table of proteins destabilizing and unweaving single-stranded DNA and a classification table of proteins bound with single-stranded DNA according to their functional significance are presented. It is stated that the problem of single-stranded DNA significance in cells remains open, although some results have been achieved.     

Gene clusters and polycistronic transcription in eukaryotes

Sometimes genes are arranged nonrandomly on the chromosomes of eukaryotes. This review considers instances of gene clusters in which two genes or more are expressed from a single promoter. This includes cases in which a polycistronic pre-mRNA is processed to make monocistronic mRNAs in nematodes, as well as isolated examples of polycistronic mRNAs found in mammals, flies, and perhaps plants. BioEssays 20 :480–487, 1998. © 1998 John Wiley & Sons, Inc.