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A Dynamic E. coli Genome: Widespread DNA Contacts Revealed by Monitoring Mu Transposition

73 Pages Posted: 26 Feb 2019 Sneak Peek Status: Review Complete

See all articles by David Walker

David Walker

University of Texas at Austin - Department of Molecular Biosciences

Renat Ahatov

University of Texas at Austin - Department of Molecular Biosciences

Rasika M. Harshey

University of Texas at Austin - Department of Molecular Biosciences

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Abstract

The problem of compacting genomes while still performing cellular processes is common to all life forms. The current view for E. coli is a compacted genome with well-organized domains where replication initiates and terminates. Some studies have suggested that these and other regions are sequestered or compartmentalized such that there is little to no interaction between them. In this work, we have exploited the high efficiency and promiscuity of phage Mu transposition to directly measure the in vivo rates of interactions between genomic loci, and have developed new tools for analyzing the proximity of loci across the genome. We observe widespread contacts between all regions of the E. coli chromosome, revealing a dynamic, effectively un-compartmentalized genome. We detect long-range interactions between several genes in different gene families such as dna and rrna, implicating spatial proximity of many distantly co-regulated genes for the first time in a prokaryote. We also see a higher interaction between the two halves of the chromosome during replication, consistent with the deduced proximity and higher mobility of the chromosomal arms as they segregate during replication. Our work advances a new view of genome organization in E. coli.

Suggested Citation

Walker, David and Ahatov, Renat and Harshey, Rasika M., A Dynamic E. coli Genome: Widespread DNA Contacts Revealed by Monitoring Mu Transposition (February 22, 2019). Available at SSRN: https://ssrn.com/abstract=3339899 or http://dx.doi.org/10.2139/ssrn.3339899
This is a paper under consideration at Cell Press and has not been peer-reviewed.

David Walker

University of Texas at Austin - Department of Molecular Biosciences

100 East 24th St.
Austin, TX 78712
United States

Renat Ahatov

University of Texas at Austin - Department of Molecular Biosciences

100 East 24th St.
Austin, TX 78712
United States

Rasika M. Harshey (Contact Author)

University of Texas at Austin - Department of Molecular Biosciences ( email )

100 East 24th St.
Austin, TX 78712
United States

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