Ontology highlight
ABSTRACT:
PROVIDER: PRJNA253983 | 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 | |||
| SRR1503602.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 [MNase]
| PRJNA253985 | ENA
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: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
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 (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:Metazoan transcription is controlled through either coordinated recruitment of transcription machinery to the gene promoter, or subsequently, through regulated pausing of RNA polymerase II (Pol II) in early elongation. We report that a key difference between genes that use these distinct regulatory strategies lies in the chromatin architecture specified by their DNA sequences. Pol II pausing is prominent at highly-regulated genes whose sequences inherently disfavor nucleosome formation within the gene, but favor nucleosomal occlusion of the promoter. Pausing of polymerase maintains these genes in an active state by inhibiting the formation of repressive promoter chromatin. In contrast, promoters of housekeeping genes that lack paused Pol II are deprived of nucleosomes regardless of polymerase binding, but show higher nucleosome occupancy downstream. Our results suggest that the âdefaultâ chromatin state of a gene instructs its regulation, and that highly-regulated promoters have evolved to encourage competition between nucleosomes and paused Pol II for promoter occupancy. All experiments were done using two channels per chip, comparing DNA immunoprecipitated by the indicated antibody to matching input chromatin used for affinity purification. Where appropriate, replicate data sets were averaged.
2010-10-18 | E-GEOD-20471 | biostudies-arrayexpress
Project description:To expand our understanding of the interplay of human RNA polymerase II (Pol II) promoter elements, promoter-proximal pausing, local chromatin structure, and co-transcriptional RNA processing, the 5′ and 3′ ends of nascent, capped transcripts and the locations of nearby nucleosomes were accurately identified. High-quality visualization tools revealed sequence elements defining the core promoter, sites of pausing, and nucleosome positioning across over 177,000 transcription start regions (TSRs). We found that cap methylation begins as transcripts attain a length of about 30 nt. A nuclear run-off assay was developed that utilizes the unique properties of the DNA fragmentation factor (DFF) to demonstrate the relative location of nucleosomes and paused Pol II. Our data support the conclusion that human Pol II promoters are functional TFIID binding sites with built-in downstream information directing ubiquitous promoter proximal pausing and the downstream nucleosome location.
2020-04-29 | GSE139237 | GEO
Project description:Alternative polyadenylation (APA) has been implicated in a variety of developmental and disease processes, such as stem cell differentiation and cancer. A particularly dramatic form of APA has been documented in the developing nervous system of flies and mammals, whereby a variety of neurogenic genes undergo coordinate extension of their 3’ UTRs. In Drosophila, the RNA-binding protein ELAV inhibits RNA processing at proximal polyadenylation (poly(A)) sites, thereby fostering the formation of 3’ extensions that can reach 12 kb in length. Here, we present evidence that paused Pol II plays an important role in the selective recruitment of ELAV to elongated genes. Replacing native promoters of elongated genes with heterologous promoters blocks normal 3’ extension in the nervous system, while native promoters can induce 3’ extension in ectopic tissues expressing ELAV. Computational analyses suggest that the promoter regions of elongated genes tend to contain paused Pol II and associated cis-regulatory elements such as GAGA. ELAV ChIP-Seq assays indicate pervasive binding to the promoter regions of extended genes. Our study provides the first evidence for a regulatory link between promoter-proximal pausing and APA. ELAV ChIP-Seq assays were conducted with nuclei obtained from 6-8 hr and 10-12 hr embryos
2014-11-21 | E-GEOD-63323 | biostudies-arrayexpress