Shaw, Alexander G. and Platt, Robert J. and Withers, Jennifer K. and Blüthgen, Nils and Smallbone, Kieran and Jackson, Dean A. (2009) A stochastic-hybrid Model of DNA replication in mammalian cells. [MIMS Preprint]
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Abstract
Background This study presents a mathematical model which explores the mechanisms of human S phase that link different patterns of synthesis with the temporal S phase programme, which is seen in vivo. A chromosome and genome-wide scale is used in the modelling, which focuses on the behaviour of replication factories relative to the chromatin template. DNA foci that contain ~1Mbp of DNA are the functional units of synthesis and provide targets for the synthetic process, with each focus containing clusters of replicons that are replicated together within a single dedicated replication factory. Results The model indicates that random replication factory placement and/or dynamics cannot lead to the observed S phase progression pattern. However, co-ordination of factory activation according to Giemsa staining bands, with bias towards R-bands over G-bands, results in a transition from R- to G-band replication after 3-5hours. Our model predicts that factories move between chromosomes to avoid non-uniform entry into late S-phase. The distribution of replicons has a strong influence on simulations, with grouping of similar sized replicons making replication more efficient. Conclusions Mathematical modelling of the mammalian cell S phase provides insight into the organisation of the human genome. For example, the co-ordinated targeting of replication factories to R- and G-bands based on their structural properties and distribution in nuclei can explain the temporal progression of synthesis that is observed in experimental studies. However, further understanding of the S phase programme is likely to require additional spatial information and incorporate a three dimensional approach.
| Item Type: | MIMS Preprint |
|---|---|
| Subjects: | MSC 2010, the AMS's Mathematics Subject Classification > 92 Biology and other natural sciences |
| Depositing User: | Dr Kieran Smallbone |
| Date Deposited: | 14 Dec 2009 |
| Last Modified: | 08 Nov 2017 18:18 |
| URI: | https://eprints.maths.manchester.ac.uk/id/eprint/1368 |
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