Calculation of Chromosome Structures: In order to gain a more system-wide view of chromatin structure within the cell we are exploiting similar computational approaches (to those used to determine structural models of protein complexes) to studies of the global structure of chromatin. A chromatin conformation capture (3C) experiment, called Hi-C, is being used to provide spatial restraints on the structure. In these experiments restriction fragment digestion of DNA in intact nuclei is followed by the ligation of free DNA ends that are in close 3D spatial proximity. These ligated DNA junctions are then identified by high-throughput sequencing to provide distance restraints for structure calculations of chromatin architecture in the nucleus. Our initial studies have focussed on calculating the 3D structure of the X chromosome in stably differentiated cells.
- Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. T. Nagano, Y. Lubling, T. J. Stevens, S. Schoenfelder, E. Yaffe, W. Dean, E. D. Laue, A. Tanay, P. Fraser, Nature, 2013, 502: 59-64