Two-State Stochastic Model of In Vivo Observations of Transcriptional Bursts

IF 1.5 4区 物理与天体物理 Q2 PHYSICS, MULTIDISCIPLINARY
Luiz Guilherme S. da Silva, Romain Yvinec, Guilherme Prata, Varshant Dhar, John Reinitz, Alexandre F. Ramos
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引用次数: 0

Abstract

In vivo measurements of gene expression in single cells show behavior that has been interpreted as stochastic bursts of transcription. In one case, these data have been interpreted as random ON–OFF transitions of the gene, but there is no experimental measurements or theoretical treatment of the number of transcripts produced at each burst event. In another case, such data have been interpreted to indicate multiple underlying transcriptional states. Here, we place both of these experiments in a common theoretical framework. In it, we couple two stochastic processes, one for synthesis of transcripts and one for their removal. Analysis of the resulting model is greatly aided by the existence of exact solutions of the master equation. We find the bursting limit of the exact solutions for our two-state gene expression model and show the occurrence of bursts of multiple sizes and durations by exact stochastic simulations. We also demonstrate that data from Drosophila melanogaster interpreted in terms of multiple underlying transcription states is fully compatible with underlying two-state ON or OFF transcriptional behavior. We discuss what experimental data is required to unambiguously determine the number of underlying promoter states.

体内转录爆发观察的双态随机模型
单细胞中基因表达的体内测量显示,这种行为被解释为随机的转录爆发。在一种情况下,这些数据被解释为基因的随机开关转换,但没有实验测量或理论处理在每次爆发事件中产生的转录本数量。在另一种情况下,这些数据被解释为表明多种潜在的转录状态。在这里,我们把这两个实验放在一个共同的理论框架中。其中,我们结合了两个随机过程,一个用于转录本的合成,另一个用于转录本的去除。主方程的精确解的存在极大地帮助了结果模型的分析。我们找到了双态基因表达模型精确解的爆发极限,并通过精确随机模拟显示了多种大小和持续时间的爆发的发生。我们还证明,根据多种潜在转录状态解释的来自果蝇的数据与潜在的两状态ON或OFF转录行为完全兼容。我们讨论了需要什么实验数据来明确地确定潜在启动子状态的数量。
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来源期刊
Brazilian Journal of Physics
Brazilian Journal of Physics 物理-物理:综合
CiteScore
2.50
自引率
6.20%
发文量
189
审稿时长
6.0 months
期刊介绍: The Brazilian Journal of Physics is a peer-reviewed international journal published by the Brazilian Physical Society (SBF). The journal publishes new and original research results from all areas of physics, obtained in Brazil and from anywhere else in the world. Contents include theoretical, practical and experimental papers as well as high-quality review papers. Submissions should follow the generally accepted structure for journal articles with basic elements: title, abstract, introduction, results, conclusions, and references.
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