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Josh Lawrimore (right) and Kerry Bloom (left) with their colleagues in Applied Math-Benjamin Walker, David Adalsteinsson, Greg Forest, Dane Taylor, and Caitlin Hult have a new publication in PLOS Computational Biology. The publication is titled: “Transient crosslinking kinetics optimize gene cluster interactions”.

Abstract:  The spatiotemporal organization of the genome plays an important role in cellular processes involving DNA, but remains poorly understood, especially in the nucleolus, which does not facilitate conventional techniques. We consider here a polymer bead-chain model of the full yeast genome, featuring special dynamic crosslinking to model the effects of condensin in the nucleolus, and investigate how the kinetic timescale on which the crosslinks bind and unbind affects the resulting dynamics inside the nucleolus. When this timescale is sufficiently short, large, stable clusters appear, but when it is long, there is no resulting structure. We find that there additionally exists a range of timescales for which flexible clusters appear, in which beads frequently enter and leave clusters. These flexible clusters maximize the cross-communication between beads in the nucleolus. We apply network temporal community detection algorithms to identify what beads are in what communities at what times, in a way that is more robust and objective in comparison to conventional visual-based methods.

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