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DNA replication origin activation in space and time

Nature Reviews Molecular Cell Biology volume 16, pages 360–374 (2015)Cite this article

Subjects

Key Points

  • Activation of initiation of DNA replication occurs at only a subset of replication origins that were previously assembled in the G1 phase of the cell cycle. This is achieved through a highly regulated sequential two-step process: origin licensing in the G1 phase and origin activation during the S phase.

  • DNA replication origins from Saccharomyces cerevisiae have a sequence consensus, whereas metazoan origins are more plastic and are determined by both sequence preferences, such as G-rich elements, and epigenetic features. Chromosomal environment and transcriptional status also influence the activation of origins.

  • Origins selected in adjacent replication units are synchronously activated and form replication domains, which are activated at specific times during the S phase. Replication timing domains correlate with topologically associated domains (TADs).

  • Replication timing is regulated by specific proteins and chromatin marks.

  • The activation of DNA replication origins is developmentally controlled.

  • Specific checkpoints regulate the initiation of DNA replication in response to replication stress.

Abstract

DNA replication begins with the assembly of pre-replication complexes (pre-RCs) at thousands of DNA replication origins during the G1 phase of the cell cycle. At the G1–S-phase transition, pre-RCs are converted into pre-initiation complexes, in which the replicative helicase is activated, leading to DNA unwinding and initiation of DNA synthesis. However, only a subset of origins are activated during any S phase. Recent insights into the mechanisms underlying this choice reveal how flexibility in origin usage and temporal activation are linked to chromosome structure and organization, cell growth and differentiation, and replication stress.

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Figure 1: Formation and activation of DNA replication origins.
Figure 2: Organization of replication origins and origin flexibility.
Figure 3: Nuclear organization and replication timing in mammals.
Figure 4: Local activation and global inhibition of origin activation following replication stress.

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Acknowledgements

Research in the authors' laboratory was supported by the European Research Council (FP7/2007-2013 Grant Agreement no. 233339). This work was also supported by the ARC and the 'Ligue Nationale Contre le Cancer' (LNCC).

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  1. Olivier Ganier and Philippe Coulombe: These authors contributed equally to this work.

Authors and Affiliations

  1. Institute of Human Genetics, CNRS, 141 rue de la Cardonille, Montpellier, 34396, France

    Michalis Fragkos, Olivier Ganier, Philippe Coulombe & Marcel Méchali

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  1. Michalis Fragkos
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  2. Olivier Ganier
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Correspondence to Marcel Méchali.

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PowerPoint slides

Glossary

Replication forks

Structures that are created by unwinding of the double helix at a replication origin, from which DNA synthesis will progress in opposite directions.

CpG islands

Short DNA sequences (at least 200 bp) with a high occurence of CpG dinucleotides (for example, a ratio of CpG observed to CpG expected >0.6). In vertebrates, these sequences are often present near the transcription initiation sites of housekeeping genes.

G quadruplexes

(G4s). Guanine-rich sequences that form a four-stranded DNA structure with tetrads of guanine stacking on top of each other. These have been well studied in telomere regions.

Open chromatin

A loose or partly decondensed chromatin structure, found in euchromatin regions that are permissive for transcription.

Proliferating cell nuclear antigen

(PCNA). A homotrimer that is involved in the processivity of DNA polymerases during DNA replication, as well as having a role in DNA repair.

DNA combing

A method in which single DNA molecules are stretched on silanized glass. This method allows the detection of genomic abnormalities such as DNA rearrangements and is also a powerful technique for detecting the spacing between replication origins and the replication fork speed.

Cohesin

A protein complex that mediates the cohesion between the sister chromatids resulting from DNA replication and is also involved in their segregation during mitosis.

Hi-C

A method to detect interactions between chromatin domains in the nucleus.

Episomal vectors

Extrachromosomal DNA molecules that are able to replicate autonomously in the cell and persist without being integrated in the chromosomes. They can permit retention and expression of transgenes.

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Fragkos, M., Ganier, O., Coulombe, P. et al. DNA replication origin activation in space and time. Nat Rev Mol Cell Biol 16, 360–374 (2015). https://doi.org/10.1038/nrm4002

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