Streptococcus pneumoniae R6
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA311344 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3158170.fastq.gz | Fastqsanger.gz | |||
| SRR3158171.fastq.gz | Fastqsanger.gz | |||
| SRR3158172.fastq.gz | Fastqsanger.gz | |||
| SRR3158173.fastq.gz | Fastqsanger.gz | |||
| SRR3158174.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene [array]
| PRJNA310880 | ENA
Project description:An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene
| PRJNA311342 | ENA
Project description:We studied the response to increased DNA-supercoiling in Streptococcus pneumoniae by using seconeolitsine (SCN), a DNA topoisomerase I inhibitor. A homeostatic transcriptional response allowing recovering of supercoiling density was observed in cells treated with subinhibitory SCN concentrations. Supercoiling increases up to 40.7% (6 µM SCN) and 72.9% (8 µM SCN) were reverted to 8.5% and 44.1%, respectively. Likewise, recovery of viability and DNA-supercoiling were observed when cells were treated with those SCN concentrations and the drug was removed. The main DNA topoisomerase gene affected was topA, whose transcription depended on the supercoiling level. A two stage global transcriptomic response with 8 µM seconeolitsine was detected. The early stage (5 and 15 min, 10% of the genome) represented a response induced by increased supercoiling. The second stage represented supercoiling recovery (30 min, 2.0% of the genome). Almost 25% of the early responsive genes formed clusters with coordinated transcriptional regulation. Twelve clusters were evident, with sizes of 6.7 to 31.4 Kb (9 to 22 responsive genes). Strikingly, clusters did not contradict those observed under DNA relaxation, suggesting that bacteria manage supercoiling stress using overlapping responses. This is the first study describing a global transcriptomic response triggered by an increase in DNA supercoiling in bacteria. Total RNA was extracted from S. pneumoniae R6 cultures during exponential growth and used for RNA-Seq. Two independent replicates per condition were performed.
2016-07-07 | E-GEOD-77748 | biostudies-arrayexpress
Project description:We studied the response to increased DNA-supercoiling in Streptococcus pneumoniae by using seconeolitsine (SCN), a DNA topoisomerase I inhibitor. A homeostatic transcriptional response allowing recovering of supercoiling density was observed in cells treated with subinhibitory SCN concentrations. Supercoiling increases up to 40.7% (6 µM SCN) and 72.9% (8 µM SCN) were reverted to 8.5% and 44.1%, respectively. Likewise, recovery of viability and DNA-supercoiling were observed when cells were treated with those SCN concentrations and the drug was removed. The main DNA topoisomerase gene affected was topA, whose transcription depended on the supercoiling level. A two stage global transcriptomic response with 8 µM seconeolitsine was detected. The early stage (5 and 15 min, 10% of the genome) represented a response induced by increased supercoiling. The second stage represented supercoiling recovery (30 min, 2.0% of the genome). Almost 25% of the early responsive genes formed clusters with coordinated transcriptional regulation. Twelve clusters were evident, with sizes of 6.7 to 31.4 Kb (9 to 22 responsive genes). Strikingly, clusters did not contradict those observed under DNA relaxation, suggesting that bacteria manage supercoiling stress using overlapping responses. This is the first study describing a global transcriptomic response triggered by an increase in DNA supercoiling in bacteria. RNA was extracted from S. pneumoniae R6 cultures during exponential growth, amplified and used for microarray hibridization. Two independent replicates were performed.
2016-07-07 | E-GEOD-77587 | biostudies-arrayexpress
Project description:We studied the response to increased DNA-supercoiling in Streptococcus pneumoniae by using seconeolitsine (SCN), a DNA topoisomerase I inhibitor. A homeostatic transcriptional response allowing recovering of supercoiling density was observed in cells treated with subinhibitory SCN concentrations. Supercoiling increases up to 40.7% (6 µM SCN) and 72.9% (8 µM SCN) were reverted to 8.5% and 44.1%, respectively. Likewise, recovery of viability and DNA-supercoiling were observed when cells were treated with those SCN concentrations and the drug was removed. The main DNA topoisomerase gene affected was topA, whose transcription depended on the supercoiling level. A two stage global transcriptomic response with 8 µM seconeolitsine was detected. The early stage (5 and 15 min, 10% of the genome) represented a response induced by increased supercoiling. The second stage represented supercoiling recovery (30 min, 2.0% of the genome). Almost 25% of the early responsive genes formed clusters with coordinated transcriptional regulation. Twelve clusters were evident, with sizes of 6.7 to 31.4 Kb (9 to 22 responsive genes). Strikingly, clusters did not contradict those observed under DNA relaxation, suggesting that bacteria manage supercoiling stress using overlapping responses. This is the first study describing a global transcriptomic response triggered by an increase in DNA supercoiling in bacteria.
2016-07-07 | GSE77748 | GEO
Project description:We studied the response to increased DNA-supercoiling in Streptococcus pneumoniae by using seconeolitsine (SCN), a DNA topoisomerase I inhibitor. A homeostatic transcriptional response allowing recovering of supercoiling density was observed in cells treated with subinhibitory SCN concentrations. Supercoiling increases up to 40.7% (6 µM SCN) and 72.9% (8 µM SCN) were reverted to 8.5% and 44.1%, respectively. Likewise, recovery of viability and DNA-supercoiling were observed when cells were treated with those SCN concentrations and the drug was removed. The main DNA topoisomerase gene affected was topA, whose transcription depended on the supercoiling level. A two stage global transcriptomic response with 8 µM seconeolitsine was detected. The early stage (5 and 15 min, 10% of the genome) represented a response induced by increased supercoiling. The second stage represented supercoiling recovery (30 min, 2.0% of the genome). Almost 25% of the early responsive genes formed clusters with coordinated transcriptional regulation. Twelve clusters were evident, with sizes of 6.7 to 31.4 Kb (9 to 22 responsive genes). Strikingly, clusters did not contradict those observed under DNA relaxation, suggesting that bacteria manage supercoiling stress using overlapping responses. This is the first study describing a global transcriptomic response triggered by an increase in DNA supercoiling in bacteria.
2016-07-07 | GSE77587 | GEO
Project description:Transcription has the capacity to modify mechanically DNA topology, DNA structure, and nucleosome arrangement. Resulting from ongoing transcription, these modifications in turn, may provide instant feedback to the transcription machinery. To substantiate the connection between transcription and DNA dynamics, we charted an ENCODE map of transcription-dependent dynamic supercoiling in human Burkitt lymphoma cells using psoralen photobinding to probe DNA topology in vivo. Dynamic supercoils spread ~1.5 kb upstream of the start sites of active genes. Low and high output promoters handle this torsional stress differently as shown using inhibitors of transcription and topoisomerases, and by chromatin immunoprecipation of RNA polymerase and topoisomerases I and II. Whereas lower outputs are managed adequately by topoisomerase I, high output promoters additionally require topoisomerase II. The genome-wide coupling between transcription and DNA topology emphasizes the importance of dynamic supercoiling for gene regulation. Raji cells: untreated and treated with DRB, CPT and BLAP. Three biological replicates per treatment, each hybridized to new array. Total: 12 samples (4 treatments x 3 replicates).
2013-02-16 | E-GEOD-43751 | biostudies-arrayexpress
Project description:Transcription has the capacity to modify mechanically DNA topology, DNA structure, and nucleosome arrangement. Resulting from ongoing transcription, these modifications in turn, may provide instant feedback to the transcription machinery. To substantiate the connection between transcription and DNA dynamics, we charted an ENCODE map of transcription-dependent dynamic supercoiling in human Burkitt lymphoma cells using psoralen photobinding to probe DNA topology in vivo. Dynamic supercoils spread ~1.5 kb upstream of the start sites of active genes. Low and high output promoters handle this torsional stress differently as shown using inhibitors of transcription and topoisomerases, and by chromatin immunoprecipation of RNA polymerase and topoisomerases I and II. Whereas lower outputs are managed adequately by topoisomerase I, high output promoters additionally require topoisomerase II. The genome-wide coupling between transcription and DNA topology emphasizes the importance of dynamic supercoiling for gene regulation.
2013-02-16 | GSE43751 | GEO
Project description:The most basic level of transcription regulation in Streptococcus pneumoniae is the organization of its chromosome in topological domains. In response to drugs that caused DNA-relaxation, a global transcriptional response was observed. Separate domains were identified depending of the transcription of their genes: up-regulated (U), down-regulated (D), non-regulated (N), and flanking (F). We show here that these distinct domains have different expression and conservation tendencies. Microarray fluorescence units under non-relaxation conditions, taken as a measure of gene transcription level, were significantly lower in F genes than in the other domains in the same range of AT content. Transcription level categorization of the domains was D>U>F. In addition, a comparison of 12 S. pneumoniae genome sequences evidenced conservation of gene composition in the U and D domains and extensive gene interchange in F domains. We tested domain organization by measuring the relaxation-mediated transcription of eight insertions of a heterologous Ptccat cassette, two in each type of domain, showing that transcription depended on their chromosomal location. Moreover, transcription from the four promoters directing the five genes involved in supercoiling homeostasis, located either in U (gyrB), D (topA), or N (gyrA and parEC) domains was analyzed both in their chromosomal locations and in a replicating plasmid. Although expression from the chromosomal PgyrB and PtopA showed the expected domain regulation, their expression was down-regulated in the plasmid, which behaved as a D domain. However, both PparE and PgyrA carried their own regulatory signals, their topology-dependent expression being equivalent in the plasmid or in the chromosome. In PgyrA a DNA bend acted as a DNA supercoiling sensor. These results revealed that DNA topology works as a general transcriptional regulator, superimposed to other kind of more specific regulatory mechanisms.
2014-12-29 | GSE58186 | GEO
Project description:Effect of supercoiling level on gene expression using LZ41 and LZ54 strains containing drug-resistant alleles of different topoisomerase genes. LZ41 strain treatment with norfloxacin strongly relaxes DNA, whereas in LZ54 strain the same treatment generates high negative supercoiling (Khodursky et al., 1995, PNAS 92:11801-5; Ziechedrich et al, 1997, Genes Dev. 11:2580-92).
2005-11-05 | E-MEXP-463 | biostudies-arrayexpress