How loop extrusion affects the flow properties of dense DNA

Loop extrusion is one of the main processes shaping chromosome organisation across the cell cycle, yet its role in regulating DNA entanglement and nucleoplasm viscoelasticity remains overlooked. We simulate entangled solutions of DNA under the action of generic Loop Extruding Factors (LEF). We find that extrusion (when exclusively intrachain) drives the formation of bottle-brush-like structures and significantly lowers the entanglement and effective viscosity of the system. In marked contrast with unextruded linear DNA, the viscosity of extruded systems scales linearly with DNA length, yielding up to 1000-fold effective fluidification. Surprisingly, considering bridging (or interchain loop extrusion) between LEFs yields a marked slowing down, eventually gellifying the solution. In this talk I will also report on in vitro microrheology experiments that we performed using dense solutions of Lambda-DNA and yeast condensin, which agree with our simulations that include bridging interactions. Our results may help to understand how LEFs contribute to actively modulate genome entanglement and viscoelasticity in vivo.

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Joey Kilbride is inviting you to a scheduled Zoom meeting.
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