Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [RNA-Seq]

ABSTRACT: Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [RNA-Seq]

PROVIDER: PRJNA914691 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR22845369_1.fastq.gz	Fastqsanger.gz
	SRR22845369_2.fastq.gz	Fastqsanger.gz
	SRR22845370_1.fastq.gz	Fastqsanger.gz
	SRR22845370_2.fastq.gz	Fastqsanger.gz
	SRR22845371_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 30

Similar Datasets

Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation

Project description:Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation

| PRJNA914680 | ENA

Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [Hi-C]

Project description: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.

2024-05-17 | GSE221497 | GEO

Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [Hi-C]

Project description:Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [Hi-C]

| PRJNA914690 | ENA

Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [ChIP-Seq]

Project description:Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [ChIP-Seq]

| PRJNA914688 | ENA

Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [RNA-Seq]

Project description: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. RNA-seq analysis to reveal the regulation process of Fur proteins.

2024-05-17 | GSE221498 | GEO

Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [ChIP-Seq]

Project description:Genomic mutations allow bacteria to adapt rapidly to adverse stress environments. The three-dimensional conformation of the genome also may play 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. ChIP-seq analysis of Fur proteins binding in the genome of ZM532.

2024-05-17 | GSE221496 | GEO

Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation.

Project description: Not available

| S-EPMC11162768 | biostudies-literature

Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-05-16 | GSE221499 | GEO

Characterization of chromosomal architecture in Arabidopsis thaliana by Chromosome Conformation Capture

Project description:Background: The packaging of long chromatin fibres in the nucleus poses a major challenge, as it must fulfil both physical and functional requirements. Until recently, insight into the chromosomal architecture of plants was mainly provided by cytogenetic studies. Complementary to these analyses, chromosome conformation technologies promise to refine and improve our view on chromosomal architecture and to provide a more generalised description of nuclear organization. Results: Employing circular chromosome conformation capture (4C), this study describes chromosomal architecture in Arabidopsis nuclei from a genome-wide perspective. Surprisingly, the linear organisation of chromosomes is reflected in the genome-wide interactome. In addition, we studied the interplay of the interactome and epigenetic marks and report that the heterochromatic knob on the short arm of chromosome 4 (hk4s) maintained a pericentromere-like interaction profile and interactome despite its euchromatic surrounding. Conclusion: Despite the extreme condensation that is necessary to pack the chromosomes into the nucleus, the Arabidopsis genome appears to be packed in a predictive manner, according to the following criteria: (i) heterochromatin and euchromatin represent two distinct interactomes, (ii) interactions between chromosomes correlates with the linear position on the chromosome arm, and (iii) distal chromosome regions have a higher potential to interact with other chromosomes. This study includes circular chromosome conformation capture (4C) sequencing information of 13 samples, present in two batches, each present in duplicates (A and B). The individual 4C sequencing information can be retrieved by the 4C primer sequence, given in the 4C primer information file.

2013-11-01 | E-GEOD-50181 | biostudies-arrayexpress

Genome architecture shapes evolutionary adaptation to DNA replication stress

Project description:Genome architecture shapes evolutionary adaptation to DNA replication stress

| PRJEB42058 | ENA