Journal article
Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome
Nucleic acids research, Vol.45(13), pp.7541-7554
07/27/2017
DOI: 10.1093/nar/gkx541
PMCID: PMC5570083
PMID: 28645155
Abstract
We describe structural models of the Escherichia coli chromosome in which the positions of all 4.6 million nucleotides of each DNA strand are resolved. Models consistent with two basic chromosomal orientations, differing in their positioning of the origin of replication, have been constructed. In both types of model, the chromosome is partitioned into plectoneme-abundant and plectoneme-free regions, with plectoneme lengths and branching patterns matching experimental distributions, and with spatial distributions of highly-transcribed chromosomal regions matching recent experimental measurements of the distribution of RNA polymerases. Physical analysis of the models indicates that the effective persistence length of the DNA and relative contributions of twist and writhe to the chromosome's negative supercoiling are in good correspondence with experimental estimates. The models exhibit characteristics similar to those of 'fractal globules,' and even the most genomically-distant parts of the chromosome can be physically connected, through paths combining linear diffusion and inter-segmental transfer, by an average of only ∼10 000 bp. Finally, macrodomain structures and the spatial distributions of co-expressed genes are analyzed: the latter are shown to depend strongly on the overall orientation of the chromosome. We anticipate that the models will prove useful in exploring other static and dynamic features of the bacterial chromosome.
Details
- Title: Subtitle
- Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome
- Creators
- William C Hacker - Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USAShuxiang Li - Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USAAdrian H Elcock - Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
- Resource Type
- Journal article
- Publication Details
- Nucleic acids research, Vol.45(13), pp.7541-7554
- Publisher
- England
- DOI
- 10.1093/nar/gkx541
- PMID
- 28645155
- PMCID
- PMC5570083
- ISSN
- 0305-1048
- eISSN
- 1362-4962
- Grant note
- U54 GM105816 / NIGMS NIH HHS R01 GM087290 / NIGMS NIH HHS
- Language
- English
- Date published
- 07/27/2017
- Academic Unit
- Physics and Astronomy; Biochemistry and Molecular Biology
- Record Identifier
- 9984024511302771
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