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Nucleic Acids Research Advance Access published online on September 2, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn533
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genome integrity, repair and replication

DNA replication timing is deterministic at the level of chromosomal domains but stochastic at the level of replicons in Xenopus egg extracts

Hélène Labit, Irène Perewoska, Thomas Germe, Olivier Hyrien and Kathrin Marheineke*

Ecole Normale Supérieure, Biology Department, Laboratory of Molecular Genetics, CNRS UMR 8541, 46, rue d’Ulm, 75005 Paris, France

*To whom correspondence should be addressed. Tel: +33 1 44 32 37 33; Fax: +33 1 44 32 39 41; Email: marheine{at}biologie.ens.fr

Received April 11, 2008. Revised August 1, 2008. Accepted August 4, 2008.

Replication origins in Xenopus egg extracts are located at apparently random sequences but are activated in clusters that fire at different times during S phase under the control of ATR/ATM kinases. We investigated whether chromosomal domains and single sequences replicate at distinct times during S phase in egg extracts. Replication foci were found to progressively appear during early S phase and foci labelled early in one S phase colocalized with those labelled early in the next S phase. However, the distribution of these two early labels did not coincide between single origins or origin clusters on single DNA fibres. The 4 Mb Xenopus rDNA repeat domain was found to replicate later than the rest of the genome and to have a more nuclease-resistant chromatin structure. Replication initiated more frequently in the transcription unit than in the intergenic spacer. These results suggest for the first time that in this embryonic system, where transcription does not occur, replication timing is deterministic at the scale of large chromatin domains (1–5 Mb) but stochastic at the scale of replicons (10 kb) and replicon clusters (50–100 kb).

Present addresses: Hélène Labit, Marie Curie Research Institute, The Chart, Oxted, Surrey RH8 0TL, UK

Thomas Germe, London Research Institute, 44 Lincoln's Inn Fields, London WC2 3PX, UK


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