ArticlePLoS genetics2015
GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters.
Article in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed.
- A transcription factor by any other name - function beyond DNA binding and transactivation.EMBO reports · 2026Review
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.PNAS nexus · 2026Article
- GAGA zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion.Nature structural & molecular biology · 2025Article
- Nascent CUT&Tag captures transcription factor binding after chromatin duplication.bioRxiv : the preprint server for biology · 2025Article
- Dual mitotic bookmarking by GAF and H3K27ac orchestrates differential propagation of cell fate memory in neural development.Nature communications · 2025Article
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.bioRxiv : the preprint server for biology · 2025Article
- Bulk-level maps of pioneer factor binding dynamics during the Drosophila maternal-to-zygotic transition.Development (Cambridge, England) · 2025Article
- Vostok: A looping factor for the organization of the regulatory genome in the Drosophila brain.Molecular cell · 2025Article
- Drosophila architectural proteins M1BP and Opbp cooperatively form the active promoter of a ribosomal protein gene.Epigenetics & chromatin · 2025Article
- Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.Nucleic acids research · 2025Article
- RNA polymerases reshape chromatin architecture and couple transcription on individual fibers.Molecular cell · 2024Article
- nucMACC: An MNase-seq pipeline to identify structurally altered nucleosomes in the genome.Science advances · 2024Article
- Exploring the reciprocity between pioneer factors and development.Development (Cambridge, England) · 2024Review
- Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei.Communications biology · 2024Article
- Article
- DNA-sequence and epigenomic determinants of local rates of transcription elongation.bioRxiv : the preprint server for biology · 2023Article
- In Silico Verification of Predicted Potential Promoter Sequences in the Rice (Plants (Basel, Switzerland) · 2023Article
- Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation.Developmental cell · 2023Article
- Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development.Nature communications · 2023Article
- Localization of the Drosophila pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression.Developmental cell · 2023Article
16 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
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. These promoters show a dramatic increase in nucleosome occupancy upon GAF depletion. These results, in conjunction with previous studies showing that GAF directly interacts with nucleosome remodelers, strongly support a model where GAF directs nucleosome displacement at the promoter and thereby allows the entry Pol II to the promoter and pause sites. This action of GAF on nucleosomes is at least partially independent of paused Pol II because intergenic GAF binding sites with little or no Pol II also show GAF-dependent nucleosome displacement. In addition, the insulator factor BEAF, the BEAF-interacting protein Chriz, and the transcription factor M1BP are strikingly enriched on those GAF-associated genes where pausing is unaffected by knock down, suggesting insulators or the alternative promoter-associated factor M1BP protect a subset of GAF-bound paused genes from GAF knock-down effects. Thus, GAF binding at promoters can lead to the local displacement of nucleosomes, but this activity can be restricted or compensated for when insulator protein or M1BP complexes also reside at GAF bound promoters.
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