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| Status |
Public on Apr 04, 2015 |
| Title |
GAGA Factor maintains promoters in nucleosome-free conformation and allows promoter-proximal pausing [GRO-seq] |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
Two biological replicates of nascent RNA sequencing using GROseq to map transcriptionally-engaged RNA polymerases in untreated, LacZ-RNAi (control), and GAGA factor-RNAi.
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| Contributor(s) |
Fuda NJ, Lis JT |
| Citation(s) |
25815464 |
| |
| Submission date |
Jul 01, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicholas Fuda |
| E-mail(s) |
njf6@cornell.edu
|
| Organization name |
Cornell University
|
| Department |
Molecular Biology and Genetics
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| Street address |
417 Biotechnology Building, Cornell University
|
| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL9058 |
Illumina Genome Analyzer (Drosophila melanogaster) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE58957 |
GAGA Factor maintains promoters in nucleosome-free conformation and allows promoter-proximal pausing |
|
| Relations |
| BioProject |
PRJNA253984 |
| SRA |
SRP043988 |
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