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RESEARCH PAPER
1 Department of Molecular and Cell Biology and 2 Department of Mathematics, University of California at Berkeley, Berkeley, California 94720, USA
The circular chromosome of Escherichia coli is organized into independently supercoiled loops, or topological domains. We investigated the organization and size of these domains in vivo and in vitro. Using the expression of >300 supercoiling-sensitive genes to gauge local chromosomal supercoiling, we quantitatively measured the spread of relaxation from double-strand breaks generated in vivo and thereby calculated the distance to the nearest domain boundary. In a complementary approach, we gently isolated chromosomes and examined the lengths of individual supercoiled loops by electron microscopy. The results from these two very different methods agree remarkably well. By comparing our results to Monte Carlo simulations of domain organization models, we conclude that domain barriers are not placed stably at fixed sites on the chromosome but instead are effectively randomly distributed. We find that domains are much smaller than previously reported, 
10 kb on average. We discuss the implications of these findings and present models for how domain barriers may be generated and displaced during the cell cycle in a stochastic fashion.
[Keywords: Supercoiling; topological domains; microarrays; electron microscopy; bacterial chromosome]
Received March 29, 2004; revised version accepted May 13, 2004.
3 Corresponding author.
E-MAIL ncozzare{at}socrates.berkeley.edu; FAX (510) 643-1079.
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