It is critical that all the DNA in a cell be replicated once, and only once, per cell cycle. Jacob, Brenner and Cuzin defined a replicon as the unit in which the cell controls individual acts of replication. The replicon initiates and completes synthesis once per cell cycle. Control is exerted primarily at initiation. They proposed that an initiator protein interacted with a DNA sequence, called a replicator, to start replication. The replicator can be identified genetically as a DNA sequence required for replication, whereas the origin is defined by physical or biochemical methods as the DNA sequence at which replication begins. For many replicons, such as the E. coli oriC and the autonomously replicating sequences (or ARS) in yeast, the replicator is also an origin. However, this need not be the case: the replicon for amplified chorion genes in silkmoths has an origin close to, but separable from, the replicator. Initiator proteins have now been identified for some replicons, such as the DnaA protein in E. coli and the Origin Recognition Complex in the yeast Saccharomyces cerevisiae. In both cases, they bind to the replicators, which are also origins in these two species.
The replicator is a sequence of DNA needed for synthesis of the rest of the DNA in a replicon. It is a control element that affects the chromosome on which it lies. We say that this element acts in cis, since the replicator and the replicon are on the same chromosome. In contrast, the initiator is a protein that can be encoded on any chromosome in a cell. Thus is acts in trans, since it does not have to be encoded on the same chromosome as the replicon that it controls. In general, a trans-acting factor is an entity, usually a protein, that can diffuse through the cell to act in regulation of a certain target, whereas a cis-acting DNA sequence is on the same chromosome as the target of control. This pattern of a trans-acting protein binding to a cis-acting site on the DNA is also seen in transcriptional control.
Figure 6.1. Components of a replicon, the unit in which the cell controls repliation.
Although E. coli has a single origin in a single replicon, eukaryotic chromosomes have multiple origins, and multiple replicons. Consider a line of mammalian cells growing in culture that has an S phase of 5 hr, i.e. all the genome is replicated in 5 hr. The haploid genome size is 3 x 109 bp. If the rate of replication fork movement in this cell lines is 2000 bp per min, how many replication origins are required to replicate the entire haploid genome during S phase? Assume that two replication forks emerge from each origin (this is bidirectional replication, see below).
Experimental approaches to map origins and termini of replication and to distinguish between uni‑ and bidirectional replication
Several experimental techniques have been established for finding where replication begins and ends on chromosomes, and for distinguishing between unidirectional and bidirectional replication. We will cover two major techniques.