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

Banff International Research Station for Mathematical Innovation and Discovery

<span lang=EN-US style='font-family:Arial; color:#222222;background:white'>David Walker and Rasika M. Harshey*<b style='mso-bidi-font-weight:normal'>, </b>Department of Molecular Biosciences<b style='mso-bidi-font-weight:normal'>, </b>University of Texas at Austin<b style='mso-bidi-font-weight:normal'>, </b>Austin, TX<span style="mso-spacerun:yes">&nbsp; </span>78712<b style='mso-bidi-font-weight: normal'><o:p></o:p></b></span></p> <p class=MsoNormal style='text-align:justify;line-height:200%'><span lang=EN-US style='font-family:Arial;color:#222222;background:white'>The problem of compacting genomes while still performing cellular processes is common to all life forms. The current view for <i style='mso-bidi-font-style:normal'>E. coli </i>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. We have exploited the high efficiency and promiscuity of phage Mu transposition to directly measure the <i style='mso-bidi-font-style: normal'>in vivo</i> rates of interactions between genomic loci, and have developed new </span><span lang=EN-US style='font-family:Arial'>tools for analyzing the proximity of loci across the genome. </span><span lang=EN-US style='font-family:Arial;mso-fareast-font-family:"Times New Roman";color:black'>We observe widespread contacts between all regions of the <i style='mso-bidi-font-style: normal'>E. coli</i> chromosome, revealing a dynamic, effectively un-compartmentalized genome. We detect l</span><span lang=EN-US style='font-family:Arial;color:#222222;background:white'>ong-range interactions between several genes in different </span><span lang=EN-US style='font-family: Arial;mso-fareast-font-family:"Times New Roman";color:black'>gene families such as <span class=SpellE><i style='mso-bidi-font-style:normal'>dna</i></span> and <span class=SpellE><i style='mso-bidi-font-style:normal'>rrna</i></span>, implicating </span><span lang=EN-US style='font-family:Arial;color:#222222;background:white'>spatial proximity of many distantly co-regulated genes for the first time in a prokaryote</span><span lang=EN-US style='font-family:Arial;mso-fareast-font-family: "Times New Roman";color:black'>. </span><span lang=EN-US style='font-family: Arial'>We also see </span><span lang=EN-US style='font-family:Arial;mso-fareast-font-family: "Times New Roman";color:black'>a higher interaction between </span><span lang=EN-US style='font-family:Arial'>the two </span><span lang=EN-US style='font-family:Arial;mso-fareast-font-family:"Times New Roman";color:black'>halves of the chromosome during replication, consistent with the deduced proximity and higher mobility of the chromosomal arms as they segregate during replication</span><span lang=EN-US style='font-family:Arial'>. Our <span style='color:#222222; background:white'>work advances a new view of genome organization in <i style='mso-bidi-font-style:normal'>E. coli</i>.</span> <span style='color:#222222; background:white'><o:p></o:p></span></span></p>

Mathematics; Biology and other natural sciences; Manifolds and cell complexes; Mathematical biology

video/mp4

Author affiliation: University of Texas at Austin

2019-09-23

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/71719

Unreviewed

http://creativecommons.org/licenses/by-nc-nd/4.0/