Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 110, Issue 5, Pages 1674-1679Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1220824110
Keywords
chromosome organization; DNA segregation; polymer conformation; computational modeling; bacterial genome
Categories
Funding
- Department of Energy (DOE) Office of Science [DE-FG02-05ER64136]
- National Science Foundation (NSF) [MCB 0923679]
- National Institutes of Health [R01-GM051426]
- Samsung Scholarship
- NSF Faculty Early Career Development Program
- DOE, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering [DE-AC02-76SF00515]
- Stanford Graduate Fellowship
- Lundbeck Foundation
- Division Of Physics
- Direct For Mathematical & Physical Scien [0847050] Funding Source: National Science Foundation
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We measured the distance between fluorescent-labeled DNA loci of various interloci contour lengths in Caulobacter crescentus swarmer cells to determine the in vivo configuration of the chromosome. For DNA segments less than about 300 kb, the mean interloci distances, < r >, scale as n(0.22), where n is the contour length, and cell-to-cell distribution of the interloci distance r is a universal function of r/n(0.22) with broad cell-to-cell variability. For DNA segments greater than about 300 kb, the mean interloci distances scale as n, in agreement with previous observations. The 0.22 value of the scaling exponent for short DNA segments is consistent with theoretical predictions for a branched DNA polymer structure. Predictions from Brownian dynamics simulations of the packing of supercoiled DNA polymers in an elongated cell-like confinement are also consistent with a branched DNA structure, and simulated interloci distance distributions predict that confinement leads to freezing of the supercoiled configuration. Lateral positions of labeled loci at comparable positions along the length of the cell are strongly correlated when the longitudinal locus positions differ by <0.16 mu m. We conclude that the chromosome structure is supercoiled locally and elongated at large length scales and that substantial cell-to-cell variability in the interloci distances indicates that in vivo crowding prevents the chromosome from reaching an equilibrium arrangement. We suggest that the force causing rapid transport of loci remote from the parS centromere to the distal cell pole may arise from the release at the polar region of potential energy within the supercoiled DNA.
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