Journal
CHROMOSOME SEGREGATION AND STRUCTURE, VOL 82, 2017
Volume 82, Issue -, Pages 101-109Publisher
COLD SPRING HARBOR LABORATORY PRESS
DOI: 10.1101/sqb.2017.82.033696
Keywords
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Funding
- National Institutes of Health General Medicine [R37GM32238, T32CA201159-01, T32GM007092-39]
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ChromoShake is a three-dimensional simulator designed to explore the range of configurational states a chromosome can adopt based on thermodynamic fluctuations of the polymer chain. Here, we refine ChromoShake to generate dynamic simulations of a DNA-based motor protein such as condensin walking along the chromatin substrate. We model walking as a rotation of DNAbinding heat-repeat proteins around one another. The simulation is applied to several configurations of DNA to reveal the consequences of mechanical stepping on taut chromatin under tension versus loop extrusion on single-tethered, floppy chromatin substrates. These simulations provide testable hypotheses for condensin and other DNA-based motors functioning along interphase chromosomes. Our model reveals a novel mechanism for condensin enrichment in the pericentromeric region of mitotic chromosomes. Increased condensin dwell time at centromeres results in a high density of pericentric loops that in turn provide substrate for additional condensin.
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