Computer Simulation of Topological Domain Formation in Chromatin
Chromatin is a complex of DNA and histone proteins, in which an organism's genetic material is stored. Whether particular genes are accessible by transcriptional machinery depends strongly on the conformation of this structure. For example, genes found within large heterochromatin domains are considerably less likely to be transcribed than those outside of it.
Experimental techniques such as Hi-C analysis allow for the production of chromosome contact maps which show the details of topological domains in chromatin. These give a high-resolution (~Kbp) view of the sizes and locations of topological domains in chromatin, however they do not completely explain what causes these domains to form in the first place.
We devise simple models to represent possible mechanisms by which chromatin could form domains. Domain formation is then simulated using molecular dynamics methods, and the validity of these models is tested by comparing the results to the existing experimental data.
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