Linking stochastic fluctuations in chromatin structure and gene expression.
Linking stochastic fluctuations in chromatin structure and gene expression.
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DOI：
10.1371/journal.pbio.1001621
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发表时间：
2013
期刊：
影响因子：
9.8
通讯作者：
Boeger H
中科院分区：
文献类型：
--
作者：
Brown CR;Mao C;Falkovskaia E;Jurica MS;Boeger H
单基因分子的电子显微镜和数学建模表明，启动子在转录有利和不利的核小体构型之间随机转换，提供了转录爆发的机制。从单个基因分子表达的mRNA和蛋白质分子的数量随时间波动。这些波动部分归因于启动子在转录活性和非活性状态之间的随机转换，导致转录以爆发的方式发生。然而，转录爆发的分子基础仍然知之甚少。通过电子显微镜从酵母的单个PHO 5基因分子，我们表明，“激活”的启动子假设在稳定状态下的替代核小体配置，包括最大的抑制性，完全核小体，和最大的非抑制性，核小体自由，配置。我们表明，所观察到的启动子核小体配置的概率是从一个简单的，本质上随机的过程中获得的核小体组装，拆卸，和位置特异性滑动，我们表明，基因表达和启动子核小体配置可以机械耦合，相关的启动子核小体动力学和基因表达波动。总之，我们的研究结果表明，转录爆发的结构基础，并提供新的见解转录调控机制和启动子核小体转换的动力学。在真核生物中，如植物、真菌和动物，DNA以或多或少的规则间隔包裹在称为核小体的基本蛋白质核心周围。这种包裹阻碍了转录，这是基因表达的第一步。通过从酵母细胞中分离PHO 5基因分子，并通过电子显微镜分析其结构，我们提供了证据表明，“核小体”完全解开，然后重新包装在一个内在的随机方式。只有包裹基因调控序列（启动子）的核小体才能被观察到解绕;在整个基因体中没有发现这样的解绕。随机解包和重新包装产生了一个替代启动子核小体构型的集合，一些有利于转录，另一些则不。越来越多的证据表明，转录发生在爆发，其中转录本被连续释放，被转录不活动的间隔打断;这可能导致基因表达的显着随机波动。虽然这种行为的机制还不清楚，但我们的研究结果现在为它提供了结构基础，表明启动子DNA从核小体的缠绕和解缠绕决定了转录爆发的基本频率。
Electron microscopy of single gene molecules and mathematical modeling shows that a promoter stochastically transitions between transcriptionally favorable and unfavorable nucleosome configurations, providing a mechanism for transcriptional bursting. The number of mRNA and protein molecules expressed from a single gene molecule fluctuates over time. These fluctuations have been attributed, in part, to the random transitioning of promoters between transcriptionally active and inactive states, causing transcription to occur in bursts. However, the molecular basis of transcriptional bursting remains poorly understood. By electron microscopy of single PHO5 gene molecules from yeast, we show that the “activated” promoter assumes alternative nucleosome configurations at steady state, including the maximally repressive, fully nucleosomal, and the maximally non-repressive, nucleosome-free, configuration. We demonstrate that the observed probabilities of promoter nucleosome configurations are obtained from a simple, intrinsically stochastic process of nucleosome assembly, disassembly, and position-specific sliding; and we show that gene expression and promoter nucleosome configuration can be mechanistically coupled, relating promoter nucleosome dynamics and gene expression fluctuations. Together, our findings suggest a structural basis for transcriptional bursting, and offer new insights into the mechanism of transcriptional regulation and the kinetics of promoter nucleosome transitions. In eukaryotes, such as plants, fungi, and animals, the DNA is wrapped around basic protein cores called nucleosomes at more or less regular intervals. This wrapping discourages transcription, the first step in gene expression. By isolating PHO5 gene molecules from yeast cells and analyzing their structure by electron microscopy, we provide evidence that the “nucleosomes” completely unwrap and then re-wrap in an intrinsically stochastic manner. Only nucleosomes that wrap the regulatory sequences of the gene (promoter) were observed to unspool; no such unspooling was found across the body of the gene. Random unwrapping and re-wrapping generates an ensemble of alternative promoter nucleosome configurations, some conducive to transcription, others not. Mounting evidence suggests that transcription occurs in bursts, where transcripts are released in close succession, interrupted by intervals of transcriptional inactivity; this may lead to significant stochastic fluctuations in gene expression. Although the mechanism of this behavior is not understood, our findings now provide a structural basis for it, suggesting that spooling and unspooling of promoter DNA from the nucleosomes determines the fundamental frequency of transcriptional bursting.
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影响因子：
64.5
作者：
CECH, T;PARDUE, ML
通讯作者：
PARDUE, ML
影响因子：
16
作者：
Dechassa ML;Sabri A;Pondugula S;Kassabov SR;Chatterjee N;Kladde MP;Bartholomew B
通讯作者：
Bartholomew B
影响因子：
64.5
作者：
Guenther, Matthew G.;Levine, Stuart S.;Young, Richard A.
通讯作者：
Young, Richard A.
DOI：
10.1126/science.1172926
发表时间：
2009-07-31
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Hodges C;Bintu L;Lubkowska L;Kashlev M;Bustamante C
通讯作者：
Bustamante C
影响因子：
5.3
作者：
Griesenbeck, J;Boeger, H;Kornberg, RD
通讯作者：
Kornberg, RD