The contribution of dormant origins to genome stability: from cell biology to human genetics

Abstract

The ability of a eukaryotic cell to precisely and accurately replicate its DNA is crucial to maintain genome stability. Here we describe our current understanding of the process by which origins are licensed for DNA replication and review recent work suggesting that fork stalling has exerted a strong selective pressure on the positioning of licensed origins. In light of this, we discuss the complex and disparate phenotypes observed in mouse models and humans patients that arise due to defects in replication licensing proteins.

Keywords: Dormant origins; MCM2–7; Meier–Gorlin; Origin licensing; Pre-RC; Replication origins.

Fig. 1

Ensuring precise chromosome replication. A small segment of chromosomal DNA is shown, consisting of three domains each replicated from three replication origins. The domain is shown at different stages of the cell cycle: G1, early-, mid- and late-S phase and G2; a whole chromosome containing the chromosomal segment is shown in mitosis (‘M’). (A) The DNA is under-replicated as a consequence of origins in the middle cluster failing to fire. As sister chromatids are separated during anaphase, the chromosome is likely to be broken near the unreplicated section. (B) Origins are correctly used and chromosomal DNA is successfully duplicated. (C) One of the origins fires for a second time in S phase. The local duplication of DNA in the vicinity of the over-firing origin represents an irreversible genetic change and might be resolved to form a tandem duplication. Reproduced from .

Fig. 2

Cartoon of replication origins near the end of a chromosome. DNA is denoted as a single black line, with a telomere (chromosome end) to the left. Prior to S phase entry, origins are licensed by binding a double hexamer of MCM2–7 proteins (blue). As an origin fires, both MCM2–7 single hexamers are converted into an active CMG helicase (pink). (A) Forks initiate at origins 1, 3 and 4. If an active fork passively replicates an inactive origin, the MCM2–7 at the inactive origin is displaced making the origin dormant (origin 2) for that particular cell cycle. (B) In case of irreversible fork stalling (denoted by a red cross) otherwise dormant origins can be activated (origin 2) to ensure complete replication of the DNA. If both of the converging forks stall (‘double fork stall’) without a dormant origin existing between them (as occurs at forks converging between origins 3 and 4), replication of the intervening DNA is compromised. If the single fork heading towards the telomere (the fork move left from origin 1) irreversibly stalls and there is no telomere-distal origin, (‘telomeric fork stall’), then this single stall event can also compromise full replication of the genome. Reproduced from .

Fig. 3

Model for how cells respond to low levels of replicative stress. Two adjacent clusters of origins (factories bounded by green circles) are shown on a single piece of DNA (black lines). Under normal circumstances (left), the upper factory is activated slightly earlier than the factory below, and each initiates three origins. Under low levels of replicative stress (right), replication forks are inhibited in the earlier replicating cluster, which promotes the firing of dormant origins as a direct consequence of stochastic origin firing. Replicative stress activates DNA damage checkpoint kinases, which preferentially inhibit the activation of the unfired later clusters/new factories. Reproduced from .

Fig. 4

The consequences of limited licensing. Mutations of pre-RC components have been organized into two groups, MCMs, and non-MCMs (blue rectangles). The biochemical consequences for these mutations are then organized into three groups: MCM loading, decreased licensing activity, and ‘other’ (green rectangles). In turn, these biochemical defects lead to more general cellular defects, decreased proliferation and genome instability (orange rectangles). Subsequently, these cellular defects manifest as a phenotype observed at the organismal level (red rectangles). The arrows drawn from mutation to biochemical defect, to cellular defect, to phenotype are colour coded in reference to the type of experimental system in which the observations have been made (red: mouse models harbouring MCM hypomorphic alleles; green: Meier Gorlin patients; blue: human MCM4 patients; black: in vitro experimental systems). Lines are dashed where assumptions are made in line with observations, but it is unclear if a direct cause and consequence can be conclusively drawn.