GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters.
GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters.
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DOI：
10.1371/journal.pgen.1005108
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发表时间：
2015-03
期刊：
影响因子：
4.5
通讯作者：
Lis JT
中科院分区：
文献类型：
--
作者：
Fuda NJ;Guertin MJ;Sharma S;Danko CG;Martins AL;Siepel A;Lis JT
先前的研究表明，GAGA因子（GAF）富集在具有暂停RNA聚合酶II（Pol II）的启动子上，但其全基因组功能和作用机制在很大程度上仍未表征。我们在对照和GAF-RNAi果蝇S2细胞中使用全局连续测序（GR 0-seq）测定了转录参与聚合酶的水平，并发现启动子近端聚合酶在大的暂停启动子子集上显著降低，其中GAF占用通过敲低降低。这些启动子显示出在GAF耗尽时核小体占据的显著增加。这些结果，结合先前的研究表明，GAF直接与核小体重塑相互作用，强烈支持的模型，其中GAF指导核小体位移的启动子，从而允许进入Pol II的启动子和暂停网站。GAF对核小体的这种作用至少部分独立于暂停的Pol II，因为具有很少或没有Pol II的基因间GAF结合位点也显示出GAF依赖的核小体置换。此外，绝缘子因子BEAF，BEAF相互作用蛋白质Chriz和转录因子M1 BP在那些GAF相关基因上显著富集，其中暂停不受敲低的影响，这表明绝缘子或替代启动子相关因子M1 BP保护GAF结合暂停基因的子集免受GAF敲低效应的影响。因此，GAF在启动子处的结合可以导致核小体的局部置换，但是当绝缘子蛋白或M1 BP复合物也驻留在GAF结合的启动子处时，这种活性可以被限制或补偿。转录调节对于响应环境变化和发育程序的适当基因表达至关重要。真核生物已经进化出多种转录因子调节转录的机制。一种机制是染色质的重组以允许Pol II募集。另一个是启动子近端暂停的Pol II的释放，其中在转录起始位点（TSS）下游20-60个碱基处停止的Pol II转录被允许通过基因体进入生产性延伸。果蝇转录因子GAF与经历暂停的基因结合，并与核小体重塑因子和暂停因子NELF相互作用。因此，GAF可以调节转录所需的多个点，但其机制作用尚未完全了解全基因组。我们从细胞中耗尽GAF，并检查了Pol II和核小体分布在基因间的全基因组变化。我们发现，GAF耗竭降低了GAF结合TSS上游的基因的聚合酶密度，并导致核小体移动到启动子区。我们的研究结果表明，GAF是重要的维持启动子的可及性，使Pol II被招募到启动子和进入暂停网站下游的TSS。因此，GAF对于提供适当控制基因表达所必需的染色质环境至关重要。
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. Transcriptional regulation is critical for proper gene expression in response to environmental changes and developmental programs. Eukaryotes have evolved multiple mechanisms by which transcription factors regulate transcription. One mechanism is the reorganization of chromatin to allow Pol II recruitment. Another is the release of promoter-proximal paused Pol II, where Pol II transcription that is halted 20–60 bases downstream of the transcription start site (TSS) is allowed to enter into productive elongation through the gene body. The Drosophila transcription factor GAF binds to genes that undergo pausing and interacts with nucleosome remodelers and the pausing factor NELF. Thus, GAF can regulate multiple points necessary for transcription, but its mechanistic role is not fully understood genome-wide. We depleted GAF from cells and examined the genome-wide changes in Pol II and nucleosome distributions across genes. We found that GAF depletion reduces polymerase density at genes where GAF binds just upstream of the TSS, and results in nucleosomes moving into the promoter region. Our results show that GAF is important for maintaining the promoter accessibility, allowing Pol II to be recruited to promoters and enter the pause sites downstream of the TSS. Thus, GAF is critical for providing the chromatin environment necessary for the proper control of gene expression.
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影响因子：
48
作者：
Kasinathan, Sivakanthan;Orsi, Guillermo A.;Zentner, Gabriel E.;Ahmad, Kami;Henikoff, Steven
通讯作者：
Henikoff, Steven
DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
8.8
作者：
Core LJ;Waterfall JJ;Gilchrist DA;Fargo DC;Kwak H;Adelman K;Lis JT
通讯作者：
Lis JT
影响因子：
5.3
作者：
Horard, B;Tatout, C;Pirrotta, V
通讯作者：
Pirrotta, V
影响因子：
5.6
作者：
Agianian, B;Leonard, K;Tucker, PA
通讯作者：
Tucker, PA