Luiz Guilherme S. da Silva, Romain Yvinec, Guilherme Prata, Varshant Dhar, John Reinitz, Alexandre F. Ramos
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Two-State Stochastic Model of In Vivo Observations of Transcriptional Bursts
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.
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.