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Eukaryotic DNA replication origins: many choices for appropriate answers

Key Points

  • At each cell division in humans, DNA replication starts from 50,000 DNA replication origins, which are at specific locations along the chromosomes and from which DNA synthesis proceeds bidirectionally. In contrast to origins in bacteria or Saccharomyces cerevisiae, a specific consensus sequence has not yet been identified in metazoans and their selection mechanism seems to be mainly epigenetic.

  • DNA replication origins have a common 12 bp consensus sequence in S. cerevisiae but only a few of them are used in vivo. In Schizosaccharomyces pombe, DNA replication origins are characterized by AT-rich islands. In metazoans, both CpG islands and AT-rich stretches may characterize the origins.

  • Replication origins are in excess relative to their use in each cell cycle. They fall into three main classes: used all the time (constitutive), used in an apparently stochastic manner in each cell cycle (flexible; most origins are of this type) and used in specific growth or differentiation conditions (dormant).

  • Replication stress and checkpoint controls can regulate the use of flexible origins and the activation of dormant origins and can repress late replication origins. Transcriptional features and development also modulate the use and position of the replication origins along the genome.

  • Chromosome structure and chromatin organization have a big impact on origin selection and function.

  • Replication origins are organized in clusters of consecutive origins that are synchronously activated.

Abstract

At each cell division in humans, 30,000–50,000 DNA replication origins are activated, and it remains unclear how they are selected and recognized by replication factors. DNA replication in multicellular organisms must accommodate variations in growth conditions and DNA damage. It must also adapt to changes in chromatin organization associated with cell differentiation and development. The selection of replication origins in metazoans seems to involve multiple choices, with the appropriate answers depending on the identity of the cell or the conditions of growth. This suggests that during evolution, the use of replication origins became more controlled by epigenetic mechanisms affecting chromosome dynamics and expression than by DNA synthesis per se.

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Figure 1: Replication origins.
Figure 2: Features of DNA replication origins.
Figure 3: Different types of DNA replication origins.
Figure 4: Checkpoint control of replication origins firing.
Figure 5: Chromatin and replication origins.
Figure 6: Selection of specific origins of DNA replication during the cell cycle.

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Acknowledgements

I would like to thank E. Andermarcher for critical reading of this manuscript. The M.M laboratory is supported by the European Research Council (ERC advanced grant FP7/2007-2013, Grant Agreement no. 233339), the ANR, the 'Association pour la Recherche contre le Cancer', and the 'Ligue Nationale contre le Cancer'.

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Glossary

Replication fork

When replication starts, the opened DNA forms two branched structures on both sides of the replication origin that resemble forks. Fork progression is mediated by the action of DNA helicases that unwind the DNA and facilitate the movement of the DNA synthesis machinery.

Checkpoint

One of many points in the cell cycle at which the cell checks whether the cycle can progress normally or should be delayed or stopped to allow time for the current phase to be completed properly.

CpG island

A genomic region of at least 200bp with a high frequency of CpG sites. CpG islands are often found in the transcription promoter regions of mammalian genomes and are unmethylated when the gene is expressed.

Chromatin immunoprecipitation

A method used to localize the DNA-binding site of a protein using an antibody that specifically recognizes the protein on chromatin, which is previously broken into small pieces.

Minichromosome maintenance protein

(MCM). One of a group of proteins that belong to the AAA+ ATPase family and have a conserved MCM box motif. The main eukaryotic DNA-dependent and ATPase-dependent DNA helicase is MCM2–7, a complex of six different MCM subunits.

GINS complex

A complex comprising four subunits — SLD5, PSF1, PSF2 and PSF3 — that are ubiquitous and evolutionarily conserved in eukaryotes. It interacts with the MCM2–7 complex and CDC45 to activate the MCM2–7 helicase activity.

DNA combing

A method used to produce arrays of uniformly stretched DNA molecules on silanized glass. The in vivo incorporation of fluorescent deoxynucleotides during replication permits, after combing, the localization of DNA replication origins and the progression of the replication forks on the combed DNA molecules.

Topoisomerase II

An enzyme that cuts and reseals both strands of DNA to remove DNA supercoiling.

Hypomorphic allele

An allele with a mutation that decreases gene expression.

Insulator element

A regulatory DNA sequence that serves as a genetic barrier to protect a gene against positional effects and the spreading of condensed chromatin or to block enhancer activity.

Y RNA

A small non-coding RNA component of the Ro ribonucleoprotein particle that is frequently recognized by antibodies present in autoimmune sera. There are four Y RNAs in humans.

Macronucleus

The larger of the two nuclei present in ciliate protozoans.

Cohesin

A protein complex that is responsible for the association of the two sister chromatids during S phase.

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Méchali, M. Eukaryotic DNA replication origins: many choices for appropriate answers. Nat Rev Mol Cell Biol 11, 728–738 (2010). https://doi.org/10.1038/nrm2976

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