Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The newly identified transcription factor M1BP ad GAGA factor orchestrate distinct mechanisms of transcriptional regulation on paused genes

ABSTRACT: The newly identified transcription factor M1BP ad GAGA factor orchestrate distinct mechanisms of transcriptional regulation on paused genes

PROVIDER: PRJNA215078 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR951914.fastq.gz	Fastqsanger.gz
	SRR951915.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Expression analysis of Drosophila S2R+ cells depleted of M1BP by RNAi

Project description:Microarray analysis of gene expression profiles in control and M1BP-depleted Drosophila S2R+ cells. The results of this analyses are reported in Li, J. and D.S. Gilmour (2013) The newly identified transcription factor M1BP ad GAGA factor orchestrate distinct mechanisms of transcriptional regulation on paused genes. The EMBO J, in press. Four biological replicates comparing total RNA isolated from M1BP-RNAi treated and LacZ-RNAi treated cells.

2013-08-13 | E-GEOD-46629 | biostudies-arrayexpress

Expression analysis of Drosophila S2R+ cells depleted of M1BP by RNAi

2013-08-13 | GSE46629 | GEO

The newly identified transcription factor M1BP ad GAGA factor orchestrate distinct mechanisms of transcriptional regulation on paused genes

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-08-13 | E-GEOD-46630 | biostudies-arrayexpress

The newly identified transcription factor M1BP ad GAGA factor orchestrate distinct mechanisms of transcriptional regulation on paused genes

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-08-13 | GSE46630 | GEO

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

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

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

ChIP-seq analysis of M1BP in Drosophila S2R+ cells

Project description:The genomic distribution of a novel transcription factor called M1BP was determined in Drosophila S2R+ cells Polyclonal antibody raised against M1BP was used to immunoprecipitate M1BP-DNA adducts generated by treating Drosophila cells with formaldehyde, lysing the cells, and shearing DNA by sonication. Immunoprecipitated DNA was sequenced using the AB SOLiD system.

2013-08-13 | E-GEOD-49842 | biostudies-arrayexpress

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

2015-04-04 | GSE58956 | GEO

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