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

Labit H, Perewoska I, Germe T, Hyrien O, Marheineke K - Nucleic Acids Res. (2008)

Bottom Line: 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.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).

View Article: PubMed Central - PubMed

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

ABSTRACT
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).

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Model of replication timing in the Xenopus in vitro system. Replication timing is maintained during subsequent S phases at the level of replication foci and large chromatin domains, but not at the level of replication origins.
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Figure 7: Model of replication timing in the Xenopus in vitro system. Replication timing is maintained during subsequent S phases at the level of replication foci and large chromatin domains, but not at the level of replication origins.

Mentions: In conclusion, we have shown that the replication timing programme is not completely random in Xenopus egg extracts in the absence of transcription. Replication foci, which correspond to stable chromosome structural units of large size (∼1 Mb), appear to fire in a reproducible sequence from one S phase to the next. This defined pattern may be underlain by large-scale differences in chromatin structure. The rDNA locus (∼4 Mb) appears to replicate on average later than the bulk of the genome, and this coincides with a particularly inaccessible chromatin structure. Once a replication focus is activated, however, origins and origin clusters within it are activated in a stochastic manner and epigenetic marks on origins are not transferred from one cycle to the next (Figure 7). Several studies in Drosophila (6) and human cells (39–41) positively correlated transcriptional status and replication time over broad regions (>100 kb). It is unclear whether active transcription promotes early replication or vice versa. Plasmid injection experiments at different stages of S phase revealed that replication timing is necessary for propagating active or repressive chromatin structures to the next cell cycle (42). Our results in the transcriptionally inactive embryonic Xenopus system suggest that replication timing of large regions might be dependent on large-scale features of chromosome structure suggesting that basic replication timing is established prior to the transcriptional activity during early development. It will be interesting to test this hypothesis in future in vivo experiments.Figure 7.


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

Labit H, Perewoska I, Germe T, Hyrien O, Marheineke K - Nucleic Acids Res. (2008)

Model of replication timing in the Xenopus in vitro system. Replication timing is maintained during subsequent S phases at the level of replication foci and large chromatin domains, but not at the level of replication origins.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553594&req=5

Figure 7: Model of replication timing in the Xenopus in vitro system. Replication timing is maintained during subsequent S phases at the level of replication foci and large chromatin domains, but not at the level of replication origins.
Mentions: In conclusion, we have shown that the replication timing programme is not completely random in Xenopus egg extracts in the absence of transcription. Replication foci, which correspond to stable chromosome structural units of large size (∼1 Mb), appear to fire in a reproducible sequence from one S phase to the next. This defined pattern may be underlain by large-scale differences in chromatin structure. The rDNA locus (∼4 Mb) appears to replicate on average later than the bulk of the genome, and this coincides with a particularly inaccessible chromatin structure. Once a replication focus is activated, however, origins and origin clusters within it are activated in a stochastic manner and epigenetic marks on origins are not transferred from one cycle to the next (Figure 7). Several studies in Drosophila (6) and human cells (39–41) positively correlated transcriptional status and replication time over broad regions (>100 kb). It is unclear whether active transcription promotes early replication or vice versa. Plasmid injection experiments at different stages of S phase revealed that replication timing is necessary for propagating active or repressive chromatin structures to the next cell cycle (42). Our results in the transcriptionally inactive embryonic Xenopus system suggest that replication timing of large regions might be dependent on large-scale features of chromosome structure suggesting that basic replication timing is established prior to the transcriptional activity during early development. It will be interesting to test this hypothesis in future in vivo experiments.Figure 7.

Bottom Line: 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.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).

View Article: PubMed Central - PubMed

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

ABSTRACT
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).

Show MeSH