DNA and chromosomes in living cells of both bacteria and eukaryotes associate wit proteins that continuously bind and dissociate. Some聽proteins affect local structure (such as histones and histone-like聽proteins), whereas others act globally to compact whole chromosomal聽segments (such as CCCTC-binding factors).
I will first show and discuss some results from Brownian dynamics聽simulations which include both DNA and its associating proteins. We will聽show that non-specific proteins have a generic tendency to cluster, and聽discuss the relevance of this finding to DNA in vivo. We will then聽present simulations of chromatin and chromosome folding in mammalian聽nuclei, in the presence of proteins with a sequence-dependent affinity聽for the chromatin fibre. While our simulations are based simply on 1D聽bioinformatic data on the DNA-protein binding landscape, they can聽accurately predict contact maps and 3D chromosome conformations, as聽assessed experimentally via chromosome conformation capture techniques聽(such as Hi-C and Capture-C).