Abstract

In this talk I will present a generic mechanism which leads to the clustering of DNA -binding proteins, on either prokaryotic DNA or eukaryotic chromatin. The clustering is driven by DNA -mediated interactions, and remarkably, does not require any affinity between the proteins, which we assume interact purely by steric repulsion. On naked DNA , small proteins cluster to form rows, whereas larger, histone-like proteins, form more disordered aggregates. On flexible fibres such as chromatin, the clustering leads to the formation of quasi-spherical foci.

Additionally I will present results from a simulation of an ensemble of Pol II polymerases and of p65 proteins (a well-characterised transcription factor) interacting with chromosomes 5, 8, 14 and 17. These interactions lead to the formation of foci, or factories, where active regions in the DNA come together. The statistics of the contacts compare favourably with 3C data on contacts made by SAMD4 on chromosome 14 and EXT1 on chromosome 8.