The base pair-scale diffusion of nucleosomes modulates binding of transcription factors
The base pair-scale diffusion of nucleosomes modulates binding of transcription factors
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核小体的碱基对尺度扩散调节转录因子的结合
DOI：
10.1073/pnas.1815424116
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Ariel Kaplan
中科院分区：
文献类型：
--
作者：
Sergei Rudnizky;Hadeel Khamis;Omri Malik;P. Melamed;Ariel Kaplan
意义由于核小体阻止转录因子(TF)与DNA的结合，它们的位置需要积极调节。核小体也可以自发地重新定位，但这一过程及其对转铁蛋白结合的影响还没有被广泛研究。在这里，我们开发了一种基于单分子光钳的方法，可以同时测量核小体扩散和Tf与同一DNA分子的结合。我们发现核小体在DNA上经历了受限的扩散，并且当掺入组蛋白变异体H2A.Z时，这种限制被解除，导致Tf结合的增加，从而进一步偏向核小体的扩散。我们的结果揭示了一种以前未描述的转录调控机制。染色质启动子的结构决定了转录因子与DNA结合的能力，从而对基因的表达水平产生深远的影响。然而，自发的核小体运动在这一过程中的作用还不完全清楚。在这里，我们以促黄体激素β亚单位基因启动子和Egr-1为模型系统，建立了一种能够同时表征核小体在dna上的碱基尺度扩散和与转铁蛋白结合的单分子光钳实验。我们的结果表明，核小体经历受限扩散，组蛋白变体H_2A.Z的掺入有助于部分解除这种限制，导致不同类型的核小体重新定位。扩散的增加导致TF结合部位的暴露，并促进其与DNA的结合，这反过来又偏向于核小体的后续运动。我们的发现表明，使用可移动的核小体作为一种一般的转录调控机制。
Significance As nucleosomes prevent binding of transcription factors (TFs) to DNA, their position needs to be actively modulated. Nucleosomes can also reposition spontaneously, but this process and its effect on TF binding have not been extensively studied. Here, we developed a method based on single-molecule optical tweezers to simultaneously measure nucleosome diffusion and TF binding to the same DNA molecule. We show that nucleosomes undergo confined diffusion on the DNA, and that the confinement is relieved upon incorporation of the histone variant H2A.Z leading to an increase in TF binding, which then further biases nucleosome diffusion. Our results shed light on a previously uncharacterized mechanism of transcriptional regulation. The structure of promoter chromatin determines the ability of transcription factors (TFs) to bind to DNA and therefore has a profound effect on the expression levels of genes. However, the role of spontaneous nucleosome movements in this process is not fully understood. Here, we developed a single-molecule optical tweezers assay capable of simultaneously characterizing the base pair-scale diffusion of a nucleosome on DNA and the binding of a TF, using the luteinizing hormone β subunit gene (Lhb) promoter and Egr-1 as a model system. Our results demonstrate that nucleosomes undergo confined diffusion, and that the incorporation of the histone variant H2A.Z serves to partially relieve this confinement, inducing a different type of nucleosome repositioning. The increase in diffusion leads to exposure of a TF’s binding site and facilitates its association with the DNA, which, in turn, biases the subsequent movement of the nucleosome. Our findings suggest the use of mobile nucleosomes as a general transcriptional regulatory mechanism.
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影响因子：
16
作者：
Xu, Ye;Ayrapetov, Marina K.;Xu, Chang;Gursoy-Yuzugullu, Ozge;Hu, Yiduo;Price, Brendan D.
通讯作者：
Price, Brendan D.
影响因子：
10.5
作者：
Gallant-Behm, Corrie L.;Ramsey, Matthew R.;Espinosa, Joaquin M.
通讯作者：
Espinosa, Joaquin M.
H2A.Z 在胚胎干细胞自我更新和分化过程中促进活性复合物和抑制复合物接触染色质。
影响因子：
23.9
作者：
Hu G;Cui K;Northrup D;Liu C;Wang C;Tang Q;Ge K;Levens D;Crane-Robinson C;Zhao K
通讯作者：
Zhao K
影响因子：
5.7
作者：
J. Zlatanova;A. Thakar
通讯作者：
J. Zlatanova;A. Thakar