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Series GSE221497 Query DataSets for GSE221497
Status Public on May 17, 2024
Title Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [Hi-C]
Organism Zymomonas mobilis
Experiment type Other
Summary Genomic mutations allow bacteria to adapt rapidly to adverse stress environments. The three-dimensional conformation of the genome also may plays an important role in transcriptional regulation and environmental adaptation. Here, using chromosome conformation capture, we investigate the high-order architecture of the Zymomonas mobilis chromosome in response to genomic mutant and ambient stimuli (acetic acid and furfural, derived from lignocellulosic hydrolysate). We find that genomic mutation only influences the local chromosome contacts, whereas stress of acetic acid and furfural restrict the long-range contacts and change the chromosome organization at domain scales significantly. Further deciphering the domain feature unveils the important transcription factors, Ferric uptake regulation (Fur) proteins, which act as nucleoid-associated proteins to promote long-range (> 200 kb) chromosomal communications and regulate the expression of genes involved in stress response. Our work suggests that ubiquitous transcription factors in prokaryotes mediate chromosome organization and regulate stress-resistance genes in bacterial adaptation.
Hi-C analysis revealed the three-dimensional conformation of Zymomonas mobilis.
 
Overall design The chromosomal conformation analysis of wild-type strain (ZM4-RM), genomic mutation strain (ZM532-RM), genomic mutation strain under environmental stress (ZM532-AF), and strains with the deletion of Fur proteins (zur and zurfur).
 
Contributor(s) He M, Chen M, Wu B, Wang W
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Submission date Dec 21, 2022
Last update date May 17, 2024
Contact name Mao Chen
E-mail(s) chenmao92@hotmail.com
Organization name Biogas Institute of Ministry of Agriculture and Rural Affairs
Street address Section 4-13, Renmin Rd. South
City Chengdu
ZIP/Postal code 610041
Country China
 
Platforms (1)
GPL32966 HiSeq X Ten (Zymomonas mobilis)
Samples (10)
GSM6876593 ZM4, RM, rep1
GSM6876594 ZM4, RM, rep2
GSM6876595 ZM532, RM, rep1
This SubSeries is part of SuperSeries:
GSE221499 Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation
Relations
BioProject PRJNA914690

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
GSE221497_Hi-C_ZM4_RM_10k.heatmap_ICed.matrix.txt.gz 418.4 Kb (ftp)(http) TXT
GSE221497_Hi-C_ZM4_RM_5kb_heatmap.mcool 4.3 Mb (ftp)(http) MCOOL
GSE221497_Hi-C_ZM532_AF_10k.heatmap_ICed.matrix.txt.gz 422.8 Kb (ftp)(http) TXT
GSE221497_Hi-C_ZM532_AF_5kb_heatmap.mcool 4.3 Mb (ftp)(http) MCOOL
GSE221497_Hi-C_ZM532_RM_10k.heatmap_ICed.matrix.txt.gz 419.0 Kb (ftp)(http) TXT
GSE221497_Hi-C_ZM532_RM_5kb_heatmap.mcool 4.4 Mb (ftp)(http) MCOOL
GSE221497_Hi-C_zur_RM_10k.heatmap_ICed.matrix.txt.gz 419.9 Kb (ftp)(http) TXT
GSE221497_Hi-C_zur_RM_5kb_heatmap.mcool 3.9 Mb (ftp)(http) MCOOL
GSE221497_Hi-C_zurfur_RM_10k.heatmap_ICed.matrix.txt.gz 418.6 Kb (ftp)(http) TXT
GSE221497_Hi-C_zurfur_RM_5kb_heatmap.mcool 3.7 Mb (ftp)(http) MCOOL
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Raw data are available in SRA
Processed data provided as supplementary file

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