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Department of Mathematical Sciences

Seminar Archives

On this page you can find information about seminars in this and previous academic years, where available on the database.

Biomathematics Seminar: Modelling 3D chromatin organisation in mammalian genomes

Presented by Davide Marenduzzo, University of Edinburgh

8 December 2015 14:00 in CM105

DNA and in living cells of both bacteria and eukaryotes associates with
proteins that continuously bind and dissociate. Some proteins affect local
structure (such as histones and histone-like proteins), whereas others
act globally to compact whole chromosomal segments (such as CCCTC-binding

I will first show and discuss some results from Brownian dynamics
simulations which include both DNA and its associating proteins. We will
show that non-specific proteins have a generic tendency to cluster, and
discuss the relevance of this finding to DNA in vivo. We will then
present simulations of chromatin and chromosome folding in mammalian
nuclei, in the presence of proteins with a sequence-dependent affinity
for the chromatin fibre. While our simulations are based simply on 1D
bioinformatic data on the DNA-protein binding landscape, they can
accurately predict contact maps and 3D chromosome conformations, as
assessed experimentally via chromosome conformation capture techniques
(such as Hi-C and Capture-C).

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