A simulation perspective on DNA condensation in bacterial and human cells
DNA isolated in its thread-like form can be two to three orders of magnitude longer than the cell in which it is embedded. Despite numerous studies into cellular processes, the mechanisms that lead to the condensation of DNA molecules are still not fully understood. We use a coarse-grained polymer physics model to study the condensation of chromosomes in two different systems: bacterial and human tissue cells.
In the case of bacterial cells, we quantify the effect of excluded volume interactions, protein crowding, DNA-binding proteins and DNA supercoiling on the entropic elasticity and dynamics of the chromosomes under compression.
In the case of human cells, we study the process that leads to the compaction of human chromosomes into well-defined large-scale loop domains. We investigate the effect on the chromosome's 3D organisation of a specific type of protein (condensins or cohesins) which performs structural maintenance of chromosome complexes. Such proteins may be viewed as mobile slip-links (proteins that bind two DNA segments and that actively move/diffuse along the DNA molecule) which create looped domains of DNA. We consider a simple model where these proteins actively move along the DNA molecule in a specific direction, and preliminary results show that the model is able to recover experimentally observed looped domains.
This is a weekly series of informal talks given primarily by members of the soft condensed matter and statistical mechanics groups, but is also open to members of other groups and external visitors. The aim of the series is to promote discussion and learning of various topics at a level suitable to the broad background of the group. Everyone is welcome to attend..