Structural Maintenance of Chromosomes (SMC) protein complexes, such as cohesin and condensin, as well as type II topoisomerases (Top2) are essential for the correct three-dimensional organisation of chromosomes. This project investigates the interplay of these proteins and how they affect the conformation of chromosomes in the budding yeast Saccharomyces cerevisiae using analyses of Hi-C experiments and polymer modelling. Analyses of Hi-C data show both previously observed activities of cohesin and condensin as well as new contact map patterns upon the co-depletion of Top2 and cohesin in metaphase and the depletion of Top2 and condensin in anaphase. These patterns include large regions of contact enrichment between chromosomal arms and sharp, arm-long stripes of contacts in the first case and curved regions of increased contact frequency in the latter. Polymer simulations of models of intertwined chromosomal arms could recapitulate some of these patterns, hinting at the possibility that the combined effects of cohesin depletion and the missing strand-passing activity of topoisomerase II could be responsible for the contact map patterns observed in Hi-C experiments
