poster: A polymer model for the quantitative reconstruction of chromosome architecture from HiC and GAM data
speaker: Guillaume Le Treut (University of California San Diego)abstract: It is widely believed that the folding of the chromosome in the nucleus has a major effect on genetic expression. For example co-regulated genes in several species have been shown to colocalize in space despite being far away on the DNA sequence. Here, I present a new method to model the three-dimensional structure of the chromosome in live cells, based on DNA-DNA interactions measured in high-throughput chromosome conformation capture experiments (Hi-C and GAM). In contrast to existing methods, this approach incorporates a polymer model, and uses directly the contact probabilities measured in Hi-C and GAM experiments rather than estimates of average distances between genomic loci. Specifically, I model the chromosome as a Gaussian polymer with harmonic interactions and extract the coupling coefficients best reproducing the experimental contact probabilities. This model allows to reproduce experimental data with high accuracy. I also show how the reconstructed model of the chromosome can be used to study chromatin organization and its dynamics.
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