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Mapping the Multiscale Organisation of Escherichia Coli Chromosome in a Hi-C-integrated Model

Abdul Wasim, Ankit Gupta, Jagannath Mondal
doi: https://doi.org/10.1101/2020.06.29.178194
Abdul Wasim
1Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences, Hyderabad 500046, India
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Ankit Gupta
1Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences, Hyderabad 500046, India
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Jagannath Mondal
1Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences, Hyderabad 500046, India
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  • For correspondence: jmondal@tifrh.res.in
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ABSTRACT

The chromosome of Escherichia Coli (E. coli) is riddled with multi-faceted complexity and its nature of organization is slowly getting recognised. The emergence of chromosome conformation capture techniques and super-resolution microscopy are providing newer ways to explore chromosome organization, and dynamics and its effect on gene expression. Here we combine a beads-on-a-spring polymer-based framework with recently reported high-resolution Hi-C data of E. coli chromosome to develop a comprehensive model of E. coli chromosome at 5 kilo base-pair resolution. The model captures a self-organised chromosome composed of linearly organised genetic loci, and segregated macrodomains within a ring-like helicoid architecture, with no net chirality. Additionally, a genome-wide map identifies multiple chromosomal interaction domains (CIDs) and corroborates well with a transcription-centric model of the E. coli chromosome. The investigation further demonstrates that while only a small fraction of the Hi-C contacts is dictating the underlying chromosomal organization, a random-walk polymer chain devoid of Hi-C encoded contact information would fail to map the key genomic interactions unique to E. coli. Collectively, the present work, integrated with Hi-C interaction, elucidates the organization of bacterial chromosome at multiple scales, ranging from identifying a helical, macro-domain-segregated morphology at coarse-grained scale to a manifestation of CIDs at a fine-grained scale.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 26, 2020.
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Mapping the Multiscale Organisation of Escherichia Coli Chromosome in a Hi-C-integrated Model
Abdul Wasim, Ankit Gupta, Jagannath Mondal
bioRxiv 2020.06.29.178194; doi: https://doi.org/10.1101/2020.06.29.178194
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Mapping the Multiscale Organisation of Escherichia Coli Chromosome in a Hi-C-integrated Model
Abdul Wasim, Ankit Gupta, Jagannath Mondal
bioRxiv 2020.06.29.178194; doi: https://doi.org/10.1101/2020.06.29.178194

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