Numerical modeling of inhomogeneous DNA replication kinetics
Abstract
We present a calculation technique for modeling inhomogeneous DNA replication kinetics, where replication factors such as initiation rates or fork speeds can change with both position and time. We can use our model to simulate data sets obtained by molecular combing, a widely used experimental technique for probing replication. We can also infer information about the replication program by fitting our model to experimental data sets and also test the efficacy of planned experiments by fitting our model to simulated data sets. We consider asynchronous data sets and illustrate how a lack of synchrony affects replication profiles. In addition to combing data, our technique is well-adapted to microarray-based studies of replication.
Cite
@article{arxiv.1408.5216,
title = {Numerical modeling of inhomogeneous DNA replication kinetics},
author = {Michel G. Gauthier and Antoine Dubé and John Bechhoefer},
journal= {arXiv preprint arXiv:1408.5216},
year = {2014}
}
Comments
This paper was written in 2011 as a chapter for a book project that, ultimately, failed to attract enough chapters to be published. We have not updated the references or discussion to take into account the significant amount of work done in this field since then. See, for example, A. Baker and J. Bechhoefer, arxiv1312.4590 / Phys. Rev. E 89, 032703 (2014) for more recent developments