Localization of the pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression [ChIP-Seq]
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ABSTRACT:
PROVIDER: PRJNA901932 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22299955_1.fastq.gz | Fastqsanger.gz | |||
| SRR22299955_2.fastq.gz | Fastqsanger.gz | |||
| SRR22299956_1.fastq.gz | Fastqsanger.gz | |||
| SRR22299956_2.fastq.gz | Fastqsanger.gz | |||
| SRR22299957_1.fastq.gz | Fastqsanger.gz |
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Project description:The eukaryotic genome is organized to enable the precise regulation of gene expression required for development. This organization is established during early development when the embryo transitions from a fertilized germ cell to the totipotent zygote. To understand the factors and processes that drive genomic organization, we focused on the pioneer factor GAGA factor (GAF) that is required for early embryonic development in Drosophila. GAF transcriptionally activates the zygotic genome and is localized to subnuclear foci. We show that this non-uniform distribution is driven by binding to the highly abundant GA-satellite repeats. At GA-repeats, GAF is necessary to form heterochromatin and silence transcription. Thus, GAF is required to establish both active and silent regions. We propose that the foci formation enables GAF to have opposing transcriptional roles within a single nucleus. Our data support a model in which modulation of the subnuclear concentration of transcription factors acts to organize the nucleus into functionally distinct domains that are essential for the robust regulation of gene expression.
2023-06-27 | GSE218019 | GEO
Project description:Localization of the Drosophila pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression
| PRJNA901924 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-06-26 | GSE218020 | GEO
Project description:The Drosophila pioneer factor GAF is known to be essential for RNA Pol II promoter-proximal pausing and the removal of nucleosomes from a set of target promoters with GAGAG motifs. We and others have speculated that GAF recruits the ISWI family ATP-dependent chromatin remodeling complex NURF, on the basis that NURF and GAF are both required to remodel nucleosomes on an hsp70 promoter in vitro and that GAF interacts physically with NURF. However, GAF was also recently shown to interact with PBAP, a SWI/SNF family remodeler. To test which of these remodeling complexes GAF works with, we depleted GAF, NURF301, BAP170, and NURF301+BAP170 in Drosophila S2 cells using RNAi. We used a combination of PRO-seq, ATAC-seq, 3'RNA-seq, and CUT&RUN to demonstrate that while GAF and PBAP synergistically open chromatin at target promtoers which allows Pol II recruitment and pausing to proceed, GAF and NURF also synergistically position the +1 nucleosome to ensure efficient pause release and transition to productive elongation.
2020-09-01 | GSE157235 | GEO
Project description:GAF mutant larvae compare control WT larvae. To determine the effects of GAF mutation on global larval gene expression. Two-genotype experiment, WT vs. GAF mutant. 3 biological replicates
2016-07-19 | E-GEOD-67436 | biostudies-arrayexpress
Project description:Streptococcus pneumoniae is a major cause of serious infections such as pneumonia and meningitis in both children and adults worldwide. Here, we describe the development of a high-throughput genome-wide technique, Genomic Array Footprinting (GAF), for the identification of genes essential for this bacterium at various stages during infection. GAF enables negative screens by means of a combination of transposon mutagenesis and microarray technology for the detection of transposon insertion sites. We tested several methods for the identification of transposon insertion sites and found that amplification of DNA adjacent to the insertion site by PCR resulted in non-reproducible results, even when combined with an adapter. However, restriction of genomic DNA followed directly by in vitro transcription circumvented these problems. Analysis of parallel reactions generated with this method on a large mariner transposon library, showed that it was highly reproducible and correctly identified essential genes. Comparison of a mariner library to one generated with the in vivo transposition plasmid pGh:ISS1, showed that both have an equal degree of saturation, but that 9% of the genome is preferentially mutated by either one. The usefulness of GAF was demonstrated in a screen for genes essential for survival of zinc stress. This identified a gene encoding a putative cation efflux transporter, and its deletion resulted in an inability to grow under high zinc conditions. In conclusion, we developed a fast, versatile, specific, and high-throughput method for the identification of conditionally essential genes in S. pneumoniae. Keywords: GAF zinc
2007-06-26 | GSE6911 | 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: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:Nuclear RNA foci are often associated with mis-regulation of RNA processing in repeat expansion diseases. Here we report transcriptomic analysis of flies carrying expanded G4C2 repeats, the most common genetic cause of FTD/ALS. By obtaining an average of 32 million reads per library, we show that the presence of numerous nuclear G4C2 repeat RNA foci does not cause extensive changes in RNA processing in this model organism. Comparision of the transcriptomic profile of flies expressing 5R or 160R from two different chromosomes
2015-09-11 | E-GEOD-72771 | biostudies-arrayexpress
Project description:We applied a novel negative selection strategy called genomic array footprinting (GAF) to identify genes required for genetic transformation of the gram-positive bacterium Streptococcus pneumoniae. Genome-wide mariner-transposon mutant libraries in S. pneumoniae strain R6 were challenged by transformation with an antibiotic resistance cassette and growth in the presence of the corresponding antibiotic. The GAF screen identified the enrichment of mutants in two genes, i.e., hexA and hexB, and the counter-selection of mutants in 21 different genes during the challenge. Eight of the counter-selected genes were known to be essential for pneumococcal transformation. Four other genes, i.e., radA, comGF, parB, and spr2011, have previously been linked to the competence regulon, and one, spr2014, was located adjacent to the essential competence gene comFA. Directed mutants in which seven of the eight remaining genes, i.e., spr0459/spr0460, spr0777, spr0838, spr1259/spr1260, and spr1357, were deleted, displayed reduced, albeit modest, transformation rates. No connection to pneumococcal transformation could be made for the eighth gene, which encodes the response regulator RR03. We further demonstrated that the gene encoding the putative DNA repair protein RadA is required for efficient transformation of chromosomal markers, whereas transformation with replicating plasmid DNA was not significantly affected. The radA mutant also displayed an increased sensitivity to treatment with the DNA-damaging agent methyl methanesulfonate. Hence, RadA is considered to have a role in recombination of donor DNA and DNA damage repair in S. pneumoniae. Keywords: GAF competence Selection for genes essential for transformation. Aliquots of a marinerT7 transposon library generated in S. pneumoniae R6 containing approximately 40,000 independent mutants were transformed with an antibiotic resistance marker and grown without (initial library) or with (challenged library) antibiotics for 25 generation until DNA extraction.
2007-09-04 | E-GEOD-8362 | biostudies-arrayexpress