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| 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
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| 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.
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| 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).
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| Contributor(s) |
He M, Chen M, Wu B, Wang W |
| Citation(s) |
38716861 |
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| Submission date |
Dec 21, 2022 |
| Last update date |
Aug 16, 2024 |
| Contact name |
Mao Chen |
| E-mail(s) |
chenmao92@hotmail.com
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| Organization name |
Biogas Institute of Ministry of Agriculture and Rural Affairs
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| Street address |
Section 4-13, Renmin Rd. South
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| City |
Chengdu |
| ZIP/Postal code |
610041 |
| Country |
China |
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| Platforms (1) |
| GPL32966 |
HiSeq X Ten (Zymomonas mobilis) |
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| Samples (10)
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| GSM6876596 |
ZM532, RM, rep2 |
| GSM6876597 |
ZM532, AF, rep1 |
| GSM6876598 |
ZM532, AF, rep2 |
| GSM6876599 |
zur, RM, rep1 |
| GSM6876600 |
zur, RM, rep2 |
| GSM6876601 |
zurfur, RM, rep1 |
| GSM6876602 |
zurfur, RM, rep2 |
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| This SubSeries is part of SuperSeries: |
| GSE221499 |
Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation |
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| Relations |
| BioProject |
PRJNA914690 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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