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2016 ; 27
(1
): 153-66
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ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen
centromeric chromatin
#MMPMID26538024
Lawrimore J
; Aicher JK
; Hahn P
; Fulp A
; Kompa B
; Vicci L
; Falvo M
; Taylor RM 2nd
; Bloom K
Mol Biol Cell
2016[Jan]; 27
(1
): 153-66
PMID26538024
show ga
ChromoShake is a three-dimensional simulator designed to find the
thermodynamically favored states for given chromosome geometries. The simulator
has been applied to a geometric model based on experimentally determined
positions and fluctuations of DNA and the distribution of cohesin and condensin
in the budding yeast centromere. Simulations of chromatin in differing initial
configurations reveal novel principles for understanding the structure and
function of a eukaryotic centromere. The entropic position of DNA loops mirrors
their experimental position, consistent with their radial displacement from the
spindle axis. The barrel-like distribution of cohesin complexes surrounding the
central spindle in metaphase is a consequence of the size of the DNA loops within
the pericentromere to which cohesin is bound. Linkage between DNA loops of
different centromeres is requisite to recapitulate experimentally determined
correlations in DNA motion. The consequences of radial loops and cohesin and
condensin binding are to stiffen the DNA along the spindle axis, imparting an
active function to the centromere in mitosis.
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