Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA174425 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR554454_1.fastq.gz | Fastqsanger.gz | |||
| SRR554454_2.fastq.gz | Fastqsanger.gz | |||
| SRR554455_1.fastq.gz | Fastqsanger.gz | |||
| SRR554455_2.fastq.gz | Fastqsanger.gz | |||
| SRR554456_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 16 |
Similar Datasets
Project description:Global spatial organization of γ proteobacterial nucleoids is determined by specific long-range interactions.
| PRJNA173653 | ENA
Project description:GCC was used to determine the structure of E. coli grown in LB or treated with SHX. The bacterial genome is highly condensed into a nucleoid structure. Here we present global analyses of the genome spatial organization for two γ-proteobacteria: Escherichia coli and Pseudomonas aeruginosa by Genome Conformation Capture. Long distance interactions occurred within the E. coli and P. aeruginosa nucleoids with frequencies that were affected by growth condition and gene dosage. Spatial clustering of genes that are either up or down-regulated depended on the environmental signals, indicating a non-random functional organization of the nucleoid. The largest changes in gene expression upon amino acid starvation occurred in genes that participate in long-range interactions. These genes remained highly spatially clustered when transcript levels decreased. Environment specific interactions were related to DNA motifs but did not correlate with binding sites for nucleoid associated proteins. Overall we identify spatial organization as a significant factor in bacterial gene regulation and suggest that the prokaryotic operon is not simply a linear entity.
2013-05-02 | GSE40603 | GEO
Project description:Glioma contains malignant cells in diverse states. Here, we combine spatial transcriptomics with novel computational approaches to uncover the organization of glioma cellular states. We find three prominent modes of organization. First, cells in any given state tend to be spatially clustered, with local environments that are each enriched with one major cellular state. Second, specific pairs of states preferentially reside in proximity across multiple scales. Third, the pairwise interactions that we detect collectively define a global architecture composed of five layers. Hypoxia appears to drive this 5-layered organization, as it is associated with a long-range organization that extends from the hypoxic core to the infiltrative edge of the tumor. Accordingly, tumor regions distant from any hypoxic foci are less organized. In summary, we provide a conceptual framework for the organization of gliomas and highlight the role of hypoxia as a potential long-range tissue organizer.
2024-02-18 | GSE237183 | GEO
Project description:We mapped long-range chromatin interactions in embryonic stem cells (ESCs), iPSCs, and fibroblasts, and uncovered an ESC-specific genome organization that is gradually re-established during reprogramming. Confirming previous results, we show that open, accessible and closed chromatin character is the primary determinant of long-range chromatin interaction preferences. Importantly, we find that in ESCs, genomic regions extensively occupied by the pluripotency factors Oct4, Sox2, and Nanog preferentially co-localize. Similarly, regions strongly enriched for Polycomb-proteins and H3K27me3 frequently interact, and loss of the Polycomb-protein Eed diminishes these interactions without dramatically changing overall chromosome-conformation. Consistent with a spatial segregation of transcriptional networks in ESCs, Nanog and Polycomb-proteins occupy distinct nuclear spaces. Together, our data reveal that transcriptional networks that govern ESC identity play a role in genome-organization. 4C-seq was performed using a variety of baits on range of mouse cell lines, namely, ESCs, reprogrammed iPSCs, partially reprogrammed pre-iPSCs, and differentiated MEFs. Additionally, 4C-seq was performed on a partially overlapping set of baits for a Eed mutant mouse ESC line and a sibling wild-type ESC line.
2013-09-12 | E-GEOD-50029 | biostudies-arrayexpress
Project description:Gene expression is controlled under spatial chromatin structures with short-range in topologically associating domains (TAD) and long-range chromatin interactions between TADs, compartments or chromosomes, and disruption of chromatin structure leads to human diseases. The mechanism of short-range chromatin interactions has been well characterized by loop-extrusion model, but little is known about how long-range chromatin interactions are organized. Here, we demonstrate that CTCF contributes to long-range chromatin interactions via phase separation. Surprisingly, RYBP is required for the phase separation and long-range chromatin organization of CTCF. Artificial CTCF phase seperation restores the long-range chromatin interactions and corresponding gene expression which were eliminated by RYBP depletion, and manipulation of CTCF phase separation also maintains pluripotency and inhibits differentation of embryonic stem cells. These findings support a model that long-range chromatin interactions are organized through phase sepearation of architectural protein, and further reveals the distinct mechanisms of architectural protein in organizing short-range and long-range chromatin interactions.
2022-08-10 | GSE147919 | GEO
Project description:Nucleoprotein complexes play an integral role in genome organization of both eukaryotes and prokaryotes. Apart from their role in locally structuring and compacting DNA, several complexes are known to influence global organization by mediating long-range anchored chromosomal loop formation leading to spatial segregation of large sections of DNA. Such megabase (Mb) range interactions are ubiquitous in eukaryotes, but have not been demonstrated in prokaryotes. Here, using a novel genome-wide sedimentation based approach, we found that a transcription factor, Rok, forms large nucleoprotein complexes in the bacterium Bacillus subtilis. Using chromosome conformation capture (Hi-C) and live-imaging of DNA loci, we show that these complexes robustly interact with each other over large distances. Importantly, these Rok dependent long-range interactions lead to anchored chromosomal loop formation, thereby spatially isolating large sections of DNA, as previously observed for insulator proteins in eukaryotes.
2021-11-14 | GSE144475 | GEO
Project description:3D-topology of DNA in the cell nucleus provides a level of transcription regulation beyond the sequence of the linear DNA. To study the relationship between transcriptional activity and spatial environment of a gene, we have used allele-specific 4C-technology to produce high-resolution topology maps of the active and inactive X-chromosomes in female cells. We found that loci on the active X form multiple long-range interactions, with spatial segregation of active and inactive chromatin. On the inactive X, silenced loci lack preferred interactions, suggesting a unique random organization inside the inactive territory. However, escapees, among which is Xist, are engaged in long-range contacts with each other, enabling identification of novel escapees. Deletion of Xist results in partial re-folding of the inactive X into a conformation resembling the active X, without affecting gene silencing or DNA methylation. Our data point to a role for Xist RNA in shaping the conformation of the inactive X-chromosome independently of transcription. Five or six 4C viewpoints were applied on the mouse female wild type active X-chromosome, the wild type inactive X-chromosome, the conditional Xist X-chromosome and the Xist knock out X-chromosome
2011-06-24 | E-GEOD-29509 | biostudies-arrayexpress
Project description:We mapped long-range chromatin interactions in embryonic stem cells (ESCs), iPSCs, and fibroblasts, and uncovered an ESC-specific genome organization that is gradually re-established during reprogramming. Confirming previous results, we show that open, accessible and closed chromatin character is the primary determinant of long-range chromatin interaction preferences. Importantly, we find that in ESCs, genomic regions extensively occupied by the pluripotency factors Oct4, Sox2, and Nanog preferentially co-localize. Similarly, regions strongly enriched for Polycomb-proteins and H3K27me3 frequently interact, and loss of the Polycomb-protein Eed diminishes these interactions without dramatically changing overall chromosome-conformation. Consistent with a spatial segregation of transcriptional networks in ESCs, Nanog and Polycomb-proteins occupy distinct nuclear spaces. Together, our data reveal that transcriptional networks that govern ESC identity play a role in genome-organization.
2013-09-12 | GSE50029 | GEO
Project description:Analyses of the regulatory repertoire showed that distal active cis-regulatory elements (CREs) are linked to their target genes through long-range chromatin interactions with increased expression, and poised CREs are linked to their target genes through long-range chromatin interactions with depressed expression. Furthermore, we demonstrated that transcription factor MYC2 is critical for chromatin spatial organization, and proposed that MYC2 occupancy and MYC2-mediated chromatin interactions coordinately facilitate transcription within the framework of 3D chromatin architecture. An analysis of functionally related gene-defined chromatin connectivity networks revealed that genes implicated in flowering-time control are functionally compartmentalized into separate subdomains via their spatial activity in the leaf or shoot apical meristem, linking active mark- or H3K27me3-associated chromatin conformation to coordinated gene expression. The results showed that the guiding principle for modulating gene transcription in Arabidopsis includes not only the linear juxtaposition, but also the long-range chromatin interactions.
2023-07-10 | GSE233525 | GEO
Project description:Analyses of the regulatory repertoire showed that distal active cis-regulatory elements (CREs) are linked to their target genes through long-range chromatin interactions with increased expression, and poised CREs are linked to their target genes through long-range chromatin interactions with depressed expression. Furthermore, we demonstrated that transcription factor MYC2 is critical for chromatin spatial organization, and proposed that MYC2 occupancy and MYC2-mediated chromatin interactions coordinately facilitate transcription within the framework of 3D chromatin architecture. An analysis of functionally related gene-defined chromatin connectivity networks revealed that genes implicated in flowering-time control are functionally compartmentalized into separate subdomains via their spatial activity in the leaf or shoot apical meristem, linking active mark- or H3K27me3-associated chromatin conformation to coordinated gene expression. The results showed that the guiding principle for modulating gene transcription in Arabidopsis includes not only the linear juxtaposition, but also the long-range chromatin interactions.
2023-07-10 | GSE233524 | GEO