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Series GSE45966 Query DataSets for GSE45966
Status Public on Oct 30, 2013
Title High-resolution mapping of the spatial organization of Caulobacter crescentus chromosome by chromosome conformation capture in conjunction with next-generation sequencing (Hi-C)
Organism Caulobacter vibrioides CB15
Experiment type Other
Summary Chromosomes must be highly compacted and organized within cells, but how this is achieved in vivo remains poorly understood. We report the first use of Hi-C to map the structure of bacterial chromosomes at a high, unprecedented resolution. Analysis of Hi-C data and polymer modeling indicates that the Caulobacter crescentus chromosome consists of multiple, largely independent spatial domains likely comprised of supercoiled plectonemes arrayed into a bottlebrush-like fiber. These domains are stable throughout the cell cycle and re-established concomitantly with DNA replication. We provide strong evidence that domain boundaries are established by highly-expressed genes and the formation of plectoneme-free regions. Additionally, we use Hi-C to demonstrate that supercoiling, the histone-like protein HU, and SMC act at different length-scales and in complementary ways to organize and structure chromosomes within cells.
 
Overall design Hi-C experiments were performed on untreated wild type swarmer cells and drug-treated swarmer cells (Novobiocin or Rifampicin) of Caulobacter crescentus CB15N. Hi-C were also performed on swarmer cells of smc knock-out and hup1hup2 knock-out mutants of Caulobacter crescentus. Time-course Hi-C were performed on a synchronous population of Caulobacter crescentus at 5, 10, 30, 45, 60 and 75 minutes after synchronization. The progression of DNA replication during the cell cycle was followed by total genomic DNA sequencing.
 
Contributor(s) Le TB, Laub MT, Imakaev MV, Mirny LA
Citation(s) 24158908
Submission date Apr 10, 2013
Last update date May 15, 2019
Contact name Tung Ba Khanh Le
E-mail(s) tung.le@jic.ac.uk
Phone 01603450776
Organization name John Innes Centre
Department Department of Molecular Microbiology
Lab www.tunglelab.org
Street address Colney Lane
City Norwich
State/province Norfolk
ZIP/Postal code NR4 7UH
Country United Kingdom
 
Platforms (2)
GPL17001 Illumina HiSeq 2000 (Caulobacter crescentus CB15)
GPL17059 Illumina MiSeq (Caulobacter crescentus CB15)
Samples (23)
GSM1120445 Laublab_BglII_HiC_NA1000_swarmer_cell_untreated_replicate1
GSM1120446 Laublab_BglII_HiC_NA1000_swarmer_cell_untreated_replicate2
GSM1120448 Laublab_NcoI_HiC_NA1000_swarmer_cell_untreated
Relations
BioProject PRJNA196826
SRA SRP020913

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE45966_RAW.tar 11.3 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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