Polymer models of chromatin

Over the few last decades there have been incredible breakthroughs in tracking individual points on a chromosome in living cells. This has revealed that both eukaryotic and prokaryotic chromosomes are highly organized. This organization is believed to arise from protein-mediated interactions that can form both inter and intra-chromosome tethers as well as anchoring the chromosome to the membrane or protein scaffolds. A combination of theoretical and experimental techniques is required to identify the locations of these tethers.; The tethering points have an effect on the measured distances between the two fluorescently labeled points. In the case of a Gaussian polymer chain all possible arrangements of tethering along the polymer reduce to the form of a shifted Gaussian. This model depends only on an effective displacement, R&ar;eff , and an effective gyration coefficient, Leff , which refers to the effective length of the polymer between the tether and one of the fluorescent markers. The radial concentration portion of the distance distribution shows a clear tethering signature when Leff > R2eff . The commonly used mean squared distance is unable to distinguish between a tethered and a free Gaussian polymer chain.; Fluorescent markers were placed along the genome of Saccharomyces cerevisiae to address the problem of mating type switching. Data from an experiment that changed the effective binding energy between HML and MAT leads to a simple thermodynamic model of mating type switching. The fit of this model to the data predicts that the difference in free energy cost of bringing HML to MAT versus bringing HMR to MAT is 4kBT. Diffusion measurements between points on the chromatin do not show a mating type difference but result in a diffusion constant on the order of 10-4 mm2sec . These strains have also been used to plot the radial concentration between the spindle pole body and HML and also between HML and MAT. Data from the Haber lab shows a mating type difference in the radial concentration while data from Houston and Broach do not.; Tools to investigate tethered polymer model in the Escherichia coli system have been developed. This includes the creation of a plasmid that inserts the parS gene and the chloramphenicol resistance randomly into the genome of E. coli. With the origin of replication and terminus already labeled, this insertion creates a strain of E. coli with three labeled loci capable of being tracked with fluorescent proteins in three distinct colors. Custom written Matlab software is used to find the E. coli cells and extract out the positions of the spots. Preliminary analysis of one such created strain does not show a tethering signature.; A simple tethered polymer model has been applied successfully in the S. cerevisiae system. Furthermore, a collection of tools were created to apply this model to E. coli. This has led to the possibility of extracting the gyration coefficient for chromatin in living cells thereby providing important clues to its structure. The organization of chromatin can be extracted because these models have the power to locate tethering points along the chromatin. This understanding of the physical structure will shed light into the poorly understood role of structure and organization in such processes as gene regulation, recombination and chromosomal segregation.