dorsal/arxiv
View SchemaPersistence length of chromatin determines origin spacing in Xenopus early-embryo DNA replication: Quantitative comparisons between theory and experiment
| Authors | Suckjoon Jun, John Herrick, Aaron Bensimon, John Bechhoefer |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0311032 |
| URL | https://arxiv.org/abs/q-bio/0311032 |
| DOI | 10.4161/cc.3.2.655 |
| Journal | Cell Cycle 3, 223-229 (2004) |
Abstract
In Xenopus early embryos, replication origins neither require specific DNA sequences nor is there an efficient S/M checkpoint, even though the whole genome (3 billion bases) is completely duplicated within 10-20 minutes. This leads to the"random-completion problem" of DNA replication in embryos, where one needs to find a mechanism that ensures complete, faithful, timely reproduction of the genome without any sequence dependence of replication origins. We analyze recent DNA replication data in Xenopus laevis egg extracts and find discrepancies with models where replication origins are distributed independently of chromatin structure. Motivated by these discrepancies, we have investigated the role that chromatin looping may play in DNA replication. We find that the loop-size distribution predicted from a wormlike-chain model of chromatin can account for the spatial distribution of replication origins in this system quantitatively. Together with earlier findings of increasing frequency of origin firings, our results can explain the random-completion problem. The agreement between experimental data (molecular combing) and theoretical predictions suggests that the intrinsic stiffness of chromatin loops plays a fundamental biological role in DNA replication in early-embryo Xenopus in regulating the origin spacing.
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"abstract": "In Xenopus early embryos, replication origins neither require specific DNA\nsequences nor is there an efficient S/M checkpoint, even though the whole\ngenome (3 billion bases) is completely duplicated within 10-20 minutes. This\nleads to the\"random-completion problem\" of DNA replication in embryos, where\none needs to find a mechanism that ensures complete, faithful, timely\nreproduction of the genome without any sequence dependence of replication\norigins. We analyze recent DNA replication data in Xenopus laevis egg extracts\nand find discrepancies with models where replication origins are distributed\nindependently of chromatin structure. Motivated by these discrepancies, we have\ninvestigated the role that chromatin looping may play in DNA replication. We\nfind that the loop-size distribution predicted from a wormlike-chain model of\nchromatin can account for the spatial distribution of replication origins in\nthis system quantitatively. Together with earlier findings of increasing\nfrequency of origin firings, our results can explain the random-completion\nproblem. The agreement between experimental data (molecular combing) and\ntheoretical predictions suggests that the intrinsic stiffness of chromatin\nloops plays a fundamental biological role in DNA replication in early-embryo\nXenopus in regulating the origin spacing.",
"arxiv_id": "q-bio/0311032",
"authors": [
"Suckjoon Jun",
"John Herrick",
"Aaron Bensimon",
"John Bechhoefer"
],
"categories": [
"q-bio.QM",
"q-bio.BM"
],
"doi": "10.4161/cc.3.2.655",
"journal_ref": "Cell Cycle 3, 223-229 (2004)",
"title": "Persistence length of chromatin determines origin spacing in Xenopus early-embryo DNA replication: Quantitative comparisons between theory and experiment",
"url": "https://arxiv.org/abs/q-bio/0311032"
},
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