Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA174465 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:GAGA associated transcription factor (GAF) is a highly abundant and essential protein in Drosophila. GAF recognizes and binds arrays of GA dinucleotides via a zinc finger DNA binding domain to regulate transcription by binding to general TF machinery or recruit nucleosome remodeling factors. We performed GAF ChIP-seq to quantify the intensity of GAF binding at high resolution in S2 cells. In addition, we performed GAF ChIP-seq in S2 cells that were depleted of GAF by RNAi. By quantifying the degree to which all GAF binding sites are susceptible to GAF depletion, we found the cellular degree of depletion does not translate equally to the depletion of GAF at individual chromatin bound sites. For example, some high intensity GAF binding sites were completely unaffected by GAF depletion, while lower affinity binding sites were often ablated upon GAF depletion. These data sets will serve as a valuable resource to others who study the dynamic interplay between GAF and chromatin. We also compared the GAF binding sites to the full set of genomic ChIP data that is available for S2 cells and compared the intensity for each factor and histone modification/variant. Lastly, we investigated the influence that GAF had upon inducible transcription factor binding using the heat shock system.
2013-08-01 | GSE40646 | GEO
Project description:GAGA associated transcription factor (GAF) is a highly abundant and essential protein in Drosophila. GAF recognizes and binds arrays of GA dinucleotides via a zinc finger DNA binding domain to regulate transcription by binding to general TF machinery or recruit nucleosome remodeling factors. We performed GAF ChIP-seq to quantify the intensity of GAF binding at high resolution in S2 cells. In addition, we performed GAF ChIP-seq in S2 cells that were depleted of GAF by RNAi. By quantifying the degree to which all GAF binding sites are susceptible to GAF depletion, we found the cellular degree of depletion does not translate equally to the depletion of GAF at individual chromatin bound sites. For example, some high intensity GAF binding sites were completely unaffected by GAF depletion, while lower affinity binding sites were often ablated upon GAF depletion. These data sets will serve as a valuable resource to others who study the dynamic interplay between GAF and chromatin. We also compared the GAF binding sites to the full set of genomic ChIP data that is available for S2 cells and compared the intensity for each factor and histone modification/variant. Lastly, we investigated the influence that GAF had upon inducible transcription factor binding using the heat shock system. A single mock immunoprecipitation (IP) using non-specific IgG was used as a background dataset for this study (see PMID: 20844575; GSM470838). We performed two independent GAF-ChIP-seq experiments in untreated S2 cells and two replicates in S2 cells that were depleted of GAF by RNAi.
2013-08-01 | E-GEOD-40646 | biostudies-arrayexpress
Project description:ChIP-chip analysis of GAGA factor and NELF in Drosophila S2 cells
2008-04-04 | E-MEXP-1547 | 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. 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:A key model for understanding how large transcription complexes are targeted is the Drosophila dosage compensation system in which the Male-Specific Lethal (MSL) transcription complex specifically identifies and regulates the male X-chromosome. MSL complex is targeted to GA-containing sequences, but the most well-studied GA-binding transcription factor, GAGA Associated Factor (GAF), does not physically associate with MSL complex. Instead the Chromatin Linked Adapter for MSL Proteins (CLAMP) zinc-finger protein specifically targets MSL complex to GA-rich sequences on the X-chromosome. Here, we compare the binding relationships of CLAMP, GAF, and the MSL3 dosage compensation complex protein using ChIP-seq.
2018-02-01 | GSE107059 | GEO
Project description:Sequence-specific DNA-binding proteins including transcription factors (TFs) are key determinants of gene regulation and chromatin architecture. Formaldehyde cross-linking and sonication followed by Chromatin ImmunoPrecipitation (X-ChIP) and sequencing is widely used for genome-wide profiling of protein binding, but is limited by low resolution and poor specificity and sensitivity. We have implemented a simple genome-wide ChIP protocol that starts with micrococcal nuclease-digested uncross-linked chromatin followed by affinity purification and paired-end sequencing without size-selection. The resulting ORGANIC (Occupied Regions of Genomes from Affinity-purified Naturally Isolated Chromatin) profiles of the budding yeast TFs Abf1 and Reb1 achieved near-perfect accuracy, in contrast to other profiling methods, which were much less sensitive and specific. Unlike profiles produced using X-ChIP methods such as ChIP-exo, ORGANIC profiles are not biased toward identifying sites in accessible chromatin and do not require input normalization. We also demonstrate the high specificity of our method when applied to larger genomes by profiling Drosophila GAGA Factor and Pipsqueak. Taken together, these results suggest that ORGANIC profiling outperforms current X-ChIP methodologies for genome-wide profiling of TF binding sites. Chromatin immunoprecipitation of micrococcal nuclease-digested native chromatin followed by paired-end sequencing (Occupied Regions of Genomes from Affinity-purified Naturally Isolated Chromatin 'ORGANIC' profiling) of DNA-binding proteins Abf1 and Reb1 from S. cerevisiae and GAGA-binding factor (GAF) and Pipsqueak (Psq) from D. melanogaster S2 cells; and, Sono-seq (paired-end sequencing of formaldehyde cross-linked and sonicated chromatin) of yeast nuclei. Reb1 ORGANIC profiling was performed at three different salt (NaCl) concentrations (80, 150, and 600 mM) and Abf1 ORGANIC profiling was done at two different salt concentrations (80 and 600 mM) to achieve varying levels of stringency. GAF and Psq ORGANIC profiles were determined at 80 mM salt. Two replicates each of Reb1 and Abf1 600 mM ORGANIC experiments, mixed Drosophila S2 cell and S. cerevisiae nuclei Reb1 ORGANIC experiments, yeast Sono-seq, and GAF and Psq ORGANIC experiments were performed. Each S. cerevisiae and mixed S2 cell/yeast ORGANIC profiling experiment included separately sequenced input chromatin and ChIP samples. Total of 24 samples.
2013-12-14 | E-GEOD-45672 | biostudies-arrayexpress
Project description:The role of genome organization in the control of gene expression persists as a central mystery of modern biology. Most efforts have focused on the role of boundary elements and CTCF in the compartmentalization of the genome into a series of topological associating domains (TADs). These compartments have been suggested to enable long-range DNA-DNA associations via loop extrusion processes. However, there is emerging evidence for long-range focal contacts, whereby specific DNA sequences associated with promoters and distal enhancers interact to form chromatin loops. One such class of DNAs, tethering elements, binds GAGA-associated factor (GAF). Previous studies provided evidence that GAF possesses amyloid properties in vitro, enabling the formation of loops bridging separate DNA molecules. In this study we investigated the possibility that GAF also functions as a looping factor in Drosophila development. We employed a combination of Micro-C assays, proteasomal degradation, and genome editing to examine the impact of defined GAF mutants on genome topology. These studies suggest that the N-terminal POZ/BTB oligomerization domain is particularly important for long-range interactions of GAF bound to distant GAGA-rich tethering elements. By contrast, the C-terminal low complexity domain (poly Q) plays only a minor role in loop formation. The most striking effects of GAF mutants are observed for long-range promoter-promoter interactions that coordinate the activities of distant paralogous genes.
2023-02-14 | GSE218168 | GEO
Project description:We used FAIRE-seq to perform genome-wide profiling of open chromatin in 2-3 hour Drosophila embryos lacking maternal ZLD (zldM-) and in paired control embryos (yw). We demonstrate that ZLD is required to establish or maintain specific regions of open chromatin. Using single embryo RNA-seq data (from stage 5 yw and zldM- embryos) we show that loci that lose accessibility in zldM- embryos require ZLD for robust expression of associated genes. By comparing our FAIRE peaks to publicly available ChIP data (Xu et al. 2014) we demonstrate that ZLD is required for binding of the transcription factor Bicoid. To our surprise, not all ZLD-bound loci are less accessible in the mutant, suggesting that these regions rely on additional factors for open chromatin. These constitutively accessible ZLD-bound sites are enriched for the GAGA factor (GAF) binding motif, and we therefore propose that GAF may provide this additional function. We conclude that ZLD functions like a pioneer factor to define the cis-regulatory regions that drive gene expression during the MZT. Open chromatin profiling of 2-3 hour Drosophila embryos: embryos lacking maternal ZLD (zldM-, 3 replicates) and paired control embryos (yw, 2 replicates); Genomic DNA Inputs. Sequencing performed on Illumina HiSeq 2000.
2015-08-06 | E-GEOD-65837 | 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