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Series GSE163573 Query DataSets for GSE163573
Status Public on Jul 30, 2021
Title A low Smc flux avoids collisions and facilitates chromosome organization in B. subtilis
Organism Bacillus subtilis
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Summary SMC complexes are widely conserved ATP-powered loop extrusion motors indispensable for the faithful segregation of chromosomes during cell division. How SMC complexes translocate along DNA for loop extrusion and what happens when two complexes meet on the same DNA molecule is largely unknown. Revealing the origins and the consequences of SMC encounters is crucial for understanding the folding process not only of bacterial, but also of eukaryotic chromosomes. Here, we uncover several factors that influence bacterial chromosome organization by modulating the probability of such clashes. These factors include the number, the strength and the distribution of Smc loading sites, the residence time on the chromosome, the translocation rate, and the cellular abundance of Smc complexes. By studying various mutants, we show that these parameters are fine-tuned to reduce the frequency of encounters between Smc complexes, presumably as a risk mitigation strategy. Mild perturbations hamper chromosome organization by causing Smc collisions, implying that the cellular capacity to resolve them is rather limited. Altogether, we identify mechanisms that help to avoid Smc collisions and their resolution by Smc traversal or other potentially risky molecular transactions.
 
Overall design Chromosome conformation capture and ChIP-seq of Bacillus subtilis wt cells and mutants
 
Contributor(s) Anchimiuk A, Lioy VS, Boccard F, Gruber S
Citation(s) 34346312
Submission date Dec 20, 2020
Last update date Aug 20, 2021
Contact name Anna Anchimiuk
E-mail(s) stephan.gruber@unil.ch
Organization name University of Lausanne
Department Department of Fundamental Microbiology
Lab Chromosome organization and dynamics
Street address UNIL-Sorge District
City Lausanne
State/province Vaud
ZIP/Postal code 1015
Country Switzerland
 
Platforms (3)
GPL19910 Illumina HiSeq 2500 (Bacillus subtilis)
GPL24109 Illumina NextSeq 500 (Bacillus subtilis)
GPL29515 Illumina HiSeq 4000 (Bacillus subtilis)
Samples (109)
GSM4981956 3C-seq of wt cells in exponential phase in SMG at 37°C
GSM4981957 3C-seq of cells with Smc-CC435 in exponential phase in SMG at 37°C
GSM4981958 3C-seq of cells with Smc-CC431 in exponential phase in SMG at 37°C
Relations
BioProject PRJNA686787
SRA SRP298626

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
GSE163573_BSG1489_1002_3790_3803_3427_scpB_ChIP_1kb.txt.gz 188.5 Kb (ftp)(http) TXT
GSE163573_BSG3026_scpB_ChIP_1kb.txt.gz 132.0 Kb (ftp)(http) TXT
GSE163573_BSG3216_scpB_ChIP_1kb.txt.gz 119.5 Kb (ftp)(http) TXT
GSE163573_BSG3790_3805_3815_4083_4091_4100_4137_4143_parB_ChIP_1kb.txt.gz 263.5 Kb (ftp)(http) TXT
GSE163573_BSG3790_3805_3815_4083_4091_4100_4137_4143_scpB_ChIP_1kb.txt.gz 274.3 Kb (ftp)(http) TXT
GSE163573_RAW.tar 139.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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