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

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

PROVIDER: PRJNA914690 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22845745_1.fastq.gz	Fastqsanger.gz
	SRR22845745_2.fastq.gz	Fastqsanger.gz
	SRR22845746_1.fastq.gz	Fastqsanger.gz
	SRR22845746_2.fastq.gz	Fastqsanger.gz
	SRR22845747_1.fastq.gz	Fastqsanger.gz

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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

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

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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]

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

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

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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.

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Hi-C Calibration by Chemically Induced Chromosomal Interactions

Project description:The genome-wide chromosome conformation capture method, Hi-C, has greatly advanced our understanding of genome organization. However, its quantitative properties, including sensitivity, bias, and linearity, remain challenging to assess. Measuring these properties in vivo is difficult due to the heterogenous and dynamic nature of chromosomal interactions. Here, using Chemically Induced Chromosomal Interaction (CICI) method, we create stable intra- and inter-chromosomal interactions in G1-phase budding yeast across a broad range of contact frequencies. Hi-C analysis of these engineered cell populations demonstrates that static intra-chromosomal loops do not generate Topologically Associated Domains (TADs) and only promote 3D proximity within ~50kb flanking regions. At moderate sequencing depth, Hi-C is sensitive enough to detect interactions occurring in a few percent of cells. It also shows no inherent bias toward intra- versus inter-chromosomal interactions. Furthermore, we observe a linear relationship between Hi-C signal intensity and contact frequency. These findings illuminate the intrinsic properties of the Hi-C assay and provide a robust framework for its calibration.

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Hi-C of Drosophila embryos to investigate chromatin conformation during dorsal-ventral patterning

Project description:Hi-C was carried out for control embryos and embryos produced from gd7, Tollrm9/rm10, and Toll10B mutant mothers. The embryos from mutant mothers produce only a single type along the dorsal-ventral axis. We used these embryos to compare chromatin conformation across tissues.

2021-01-08 | E-MTAB-9306 | biostudies-arrayexpress

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

Project description: Not available

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HI-C 2.0: AN OPTIMIZED HI-C PROCEDURE FOR HIGH-RESOLUTION GENOME-WIDE MAPPING OF CHROMOSOME CONFORMATION

Project description:Chromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (Kb) resolution. It also includes steps to reduce random ligation and the generation of uninformative molecules, such as unligated ends, to improve the amount of valid intra-chromosomal read pairs. This protocol allows for obtaining information on conformational structures such as compartment and topologically associating domains, as well as high-resolution conformational features such as DNA loops.

2018-04-24 | GSE98161 | GEO

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