Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Drosophila melanogaster

ABSTRACT: GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes.[ChIP-seq]

PROVIDER: PRJNA289241 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR2090180.fastq.gz	Fastqsanger.gz
	SRR2090181.fastq.gz	Fastqsanger.gz
	SRR2090182.fastq.gz	Fastqsanger.gz
	SRR2090177.fastq.gz	Fastqsanger.gz
	SRR2090178.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Drosophila melanogaster

Project description:GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes. [gene expression]

| PRJNA279955 | ENA

Drosophila melanogaster

Project description:GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes. [MNase-seq]

| PRJNA289242 | ENA

GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes.

Project description:GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes.

| PRJNA289239 | ENA

GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes. [MNase-seq]

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

GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes.[ChIP-seq]

2016-07-19 | GSE70632 | GEO

Drosophila melanogaster

Project description:GAGA Factor maintains promoters in nucleosome-free conformation and allows promoter-proximal pausing [MNase]

| PRJNA253985 | ENA

Drosophila melanogaster

Project description:GAGA Factor maintains promoters in nucleosome-free conformation and allows promoter-proximal pausing [GRO-seq]

| PRJNA253984 | ENA

Nascent elongating transcript sequencing (NET-seq) show different pause registers with apyrase treatment during library preparation

Project description:Transcriptional pausing aids gene regulation by cellular RNA polymerases (RNAPs). In many bacteria, a surface-exposed domain inserted into the catalytic trigger loop (TL) of RNAP, called SI3 in Escherichia coli, modulates pausing and is essential for growth. Here we describe a viable E. coli strain lacking SI3 enabled by a suppressor TL substitution (β'Ala941→Thr; ∆SI3*). ∆SI3* increased transcription rate in vitro relative to ∆SI3, possibly explaining its viability, but retained both positive and negative effects of ∆SI3 on pausing. ∆SI3* inhibited pauses stabilized by nascent RNA structures (pause hairpins; PHs) but enhanced other pauses. Using NET-seq, we found that ∆SI3*-enhanced pauses resemble the consensus elemental pause sequence whereas sequences at ∆SI3*-suppressed pauses, which exhibited greater association with PHs, were more divergent. ∆SI3*-suppressed pauses also were associated with apparent pausing one nt upstream from the consensus sequence, often generating tandem pause sites. These '–2 pauses' were stimulated by pyrophosphate in vitro and by addition of apyrase to degrade residual NTPs during NET-seq sample processing. We propose that some pauses are readily reversible by pyrophosphorolysis or single-nucleotide cleavage. Our results document multiple ways that SI3 modulates pausing in vivo and may explain discrepancies in consensus pause sequences in some NET-seq studies.

2023-11-01 | GSE240163 | GEO

Genomic binding profiling upon expression of AbdA in S2 cells

Project description:We sought to determine the genomic binding profile of the Drosophila Hox protein AbdA in a homogenous cell system. S2-DRSC cells that have no Hox expression were stably transfected with HA-tagged AbdA under the control of a metallothionein promoter. Upon AbdA expression, we identified high enrichment of AbdA at a large number transcription start sites that colocalises with the GAGA and M1BP. Genes targeted by GAGA and M1BP contain paused RNA polymerase II and show enrichment of PcG proteins. Upon AbdA binding at M1BP-target sites, a significant reduction in PcG protein binding is observed with a concomitant reduction in RNA Pol II pausing. These data suggest that AbdA targets both GAGA- and M1BP-controlled genes, and at M1BP-controlled genes, AbdA binding is sufficient to release PcG-mediated RNA Pol II pausing to induce gene transcription.

2017-08-31 | GSE101554 | GEO

Drosophila melanogaster

Project description:Global chromatin domain organization of the Drosophila genome

| PRJNA108279 | ENA