Unknown,Transcriptomics,Genomics,Proteomics

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


ABSTRACT: 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.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Nicholas Fuda 

PROVIDER: E-GEOD-58956 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters.

Fuda Nicholas J NJ   Guertin Michael J MJ   Sharma Sumeet S   Danko Charles G CG   Martins André L AL   Siepel Adam A   Lis John T JT  

PLoS genetics 20150327 3


Previous studies have shown that GAGA Factor (GAF) is enriched on promoters with paused RNA Polymerase II (Pol II), but its genome-wide function and mechanism of action remain largely uncharacterized. We assayed the levels of transcriptionally-engaged polymerase using global run-on sequencing (GRO-seq) in control and GAF-RNAi Drosophila S2 cells and found promoter-proximal polymerase was significantly reduced on a large subset of paused promoters where GAF occupancy was reduced by knock down. Th  ...[more]

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