Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA253985 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1503610_1.fastq.gz | Fastqsanger.gz | |||
| SRR1503610_2.fastq.gz | Fastqsanger.gz | |||
| SRR1503611_1.fastq.gz | Fastqsanger.gz | |||
| SRR1503611_2.fastq.gz | Fastqsanger.gz | |||
| SRR1503612_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:GAGA Factor maintains promoters in nucleosome-free conformation and allows promoter-proximal pausing [GRO-seq]
| PRJNA253984 | ENA
Project description:Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread in higher eukaryotes. Previous studies have shown that GAF is enriched at paused genes, but the role of GAF in pausing has not been well characterized on a genome-wide level. To investigate the role of GAF in pausing, we RNAi-depleted GAF from Drosophila S2 cells, and examined the effects on promoter-proximal polymerase. We confirmed the importance of GAF for pausing on the classic pause model gene Hsp70. To determine the dependence of pausing on GAF genome-wide, we assayed the levels of transcriptionally-engaged polymerase genome-wide using GRO-seq in control and GAF-RNAi cells. We found that promoter-proximal polymerase was significantly reduced on a subset of paused genes with GAF-bound promoters. There is a dramatic change in nucleosome distribution at genes with reduction in pausing upon GAF depletion and intergenic GAF binding sites in GAF knock-down, suggesting that GAF allows the establishment of pausing at these genes by directing nucleosome displacement off of the promoter. In addition, the insulator factor BEAF, BEAF-interacting protein Chriz, and transcription M1BP enrichment on unaffected genes suggests that redundant transcription factors or insulators protect other GAF-bound paused genes from GAF knock-down effects. Three biological replicates of MNase digested chromatin from LacZ-RNAi and GAGA factor-RNAi cells.
2015-04-04 | E-GEOD-58956 | biostudies-arrayexpress
Project description:One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two thirds of genes whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are major promoter elements in mammalian cells, able to govern open chromatin conformation and support paused transcription. First, we define three classes of promoters with distinct transcriptional directionality and pausing properties which correlate with their GC content. We further analyze the direct influence of GC content on nucleosome positioning and depletion, and show that CGIs correlate with nucleosome depletion both in vivo and in vitro. We also show that transcription is not essential for nucleosome exclusion but influences both a weak +1 and a well-positioned nucleosome at CGI borders. Altogether our data support the idea that CGIs have become an essential feature of promoter structure defining novel regulatory properties in mammals. Nucleosome density and positioning were studied by high-throughput sequencing of DNA previously treated with Mnase. In parallel, chIPseq for PolII and H3K27ac were performed in mouse and human with different conditions to assess a potential effect of transcription on nucleosomes properties.
2012-06-12 | E-GEOD-38561 | biostudies-arrayexpress
Project description:One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two thirds of genes whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are major promoter elements in mammalian cells, able to govern open chromatin conformation and support paused transcription. First, we define three classes of promoters with distinct transcriptional directionality and pausing properties which correlate with their GC content. We further analyze the direct influence of GC content on nucleosome positioning and depletion, and show that CGIs correlate with nucleosome depletion both in vivo and in vitro. We also show that transcription is not essential for nucleosome exclusion but influences both a weak +1 and a well-positioned nucleosome at CGI borders. Altogether our data support the idea that CGIs have become an essential feature of promoter structure defining novel regulatory properties in mammals. Nucleosome density and positioning were studied by high-throughput sequencing of DNA previously treated with Mnase. In parallel, chIPseq for PolII and H3K27ac were performed in mouse and human with different conditions to assess a potential effect of transcription on nucleosomes properties.
2012-06-12 | E-GEOD-38563 | biostudies-arrayexpress
Project description:One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two thirds of genes whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are major promoter elements in mammalian cells, able to govern open chromatin conformation and support paused transcription. First, we define three classes of promoters with distinct transcriptional directionality and pausing properties which correlate with their GC content. We further analyze the direct influence of GC content on nucleosome positioning and depletion, and show that CGIs correlate with nucleosome depletion both in vivo and in vitro. We also show that transcription is not essential for nucleosome exclusion but influences both a weak +1 and a well-positioned nucleosome at CGI borders. Altogether our data support the idea that CGIs have become an essential feature of promoter structure defining novel regulatory properties in mammals. Nucleosome density and positioning were studied by high-throughput sequencing of DNA previously treated with Mnase. In parallel, ChIP-seq for PolII and H3K27ac were performed in mouse and human with different conditions to assess a potential effect of transcription on nucleosomes properties. To exclude a possible MNase digestion bias or sequencing artefact within CGIs, we performed additional controls such as nucleosome mapping using an alternative method based on DNA digestion by a chemical agent (phenanthroline) in human Raji B-cells.
2012-06-12 | E-GEOD-38564 | biostudies-arrayexpress
Project description:Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread in higher eukaryotes. Previous studies have shown that GAF is enriched at paused genes, but the role of GAF in pausing has not been well characterized on a genome-wide level. To investigate the role of GAF in pausing, we RNAi-depleted GAF from Drosophila S2 cells, and examined the effects on promoter-proximal polymerase. We confirmed the importance of GAF for pausing on the classic pause model gene Hsp70. To determine the dependence of pausing on GAF genome-wide, we assayed the levels of transcriptionally-engaged polymerase genome-wide using GRO-seq in control and GAF-RNAi cells. We found that promoter-proximal polymerase was significantly reduced on a subset of paused genes with GAF-bound promoters. There is a dramatic change in nucleosome distribution at genes with reduction in pausing upon GAF depletion and intergenic GAF binding sites in GAF knock-down, suggesting that GAF allows the establishment of pausing at these genes by directing nucleosome displacement off of the promoter. In addition, the insulator factor BEAF, BEAF-interacting protein Chriz, and transcription M1BP enrichment on unaffected genes suggests that redundant transcription factors or insulators protect other GAF-bound paused genes from GAF knock-down effects.
2015-04-04 | GSE58955 | GEO
Project description:Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread in higher eukaryotes. Previous studies have shown that GAF is enriched at paused genes, but the role of GAF in pausing has not been well characterized on a genome-wide level. To investigate the role of GAF in pausing, we RNAi-depleted GAF from Drosophila S2 cells, and examined the effects on promoter-proximal polymerase. We confirmed the importance of GAF for pausing on the classic pause model gene Hsp70. To determine the dependence of pausing on GAF genome-wide, we assayed the levels of transcriptionally-engaged polymerase genome-wide using GRO-seq in control and GAF-RNAi cells. We found that promoter-proximal polymerase was significantly reduced on a subset of paused genes with GAF-bound promoters. There is a dramatic change in nucleosome distribution at genes with reduction in pausing upon GAF depletion and intergenic GAF binding sites in GAF knock-down, suggesting that GAF allows the establishment of pausing at these genes by directing nucleosome displacement off of the promoter. In addition, the insulator factor BEAF, BEAF-interacting protein Chriz, and transcription M1BP enrichment on unaffected genes suggests that redundant transcription factors or insulators protect other GAF-bound paused genes from GAF knock-down effects.
2015-04-04 | GSE58956 | GEO
Project description:Promoter-proximal pausing of RNA polymerase II (RNA-Pol) is a rate-limiting step primed for rapid and synchronous induction of genes involved in critical physiological processes. Its underlying mechanisms are not fully understood. Using cytogenetic, genomic and genetic approaches, we provide evidence to support a direct role of a prevalent upstream GAGA binding factor (GAF) in transcriptional pausing of Hsp70 and many developmental regulators in Drosophila. For GAF target genes, the abundance of paused RNA-Pol and GAF is closely correlated. Promoters with higher GAF occupancy show stronger reduction of paused RNA-Pol in Gaf mutants. In addition, nucleosome organization is preferentially affected in the upstream region by GAF in a dosage-dependent manner. Genetic assays using a dominant eye phenotype caused by GAF overexpression suggests that GAF cooperates with nucleosome remodeler NURF, pausing factor NELF and an upstream binding factor BAB1. Thus, GAF plays a critical role in a regulatory network to facilitate transcriptional pausing through modulation of upstream nucleosomes.
2016-07-19 | GSE70633 | GEO
Project description:Promoter-proximal pausing of RNA polymerase II (RNA-Pol) is a rate-limiting step primed for rapid and synchronous induction of genes involved in critical physiological processes. Its underlying mechanisms are not fully understood. Using cytogenetic, genomic and genetic approaches, we provide evidence to support a direct role of a prevalent upstream GAGA binding factor (GAF) in transcriptional pausing of Hsp70 and many developmental regulators in Drosophila. For GAF target genes, the abundance of paused RNA-Pol and GAF is closely correlated. Promoters with higher GAF occupancy show stronger reduction of paused RNA-Pol in Gaf mutants. In addition, nucleosome organization is preferentially affected in the upstream region by GAF in a dosage-dependent manner. Genetic assays using a dominant eye phenotype caused by GAF overexpression suggests that GAF cooperates with nucleosome remodeler NURF, pausing factor NELF and an upstream binding factor BAB1. Thus, GAF plays a critical role in a regulatory network to facilitate transcriptional pausing through modulation of upstream nucleosomes.
2016-07-19 | GSE70632 | GEO