Volume 10, Issue 1 e1508
Advanced Review

Contributions of regulated transcription and mRNA decay to the dynamics of gene expression

Toshimichi Yamada

Toshimichi Yamada

Department of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Tokyo, Japan

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Nobuyoshi Akimitsu

Corresponding Author

Nobuyoshi Akimitsu

Isotope Science Center, University of Tokyo, Tokyo, Japan


Nobuyoshi Akimitsu, Isotope Science Center, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

Email: [email protected]

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First published: 01 October 2018
Citations: 20
Funding information JSPS Research Fellows, Grant/Award Number: 17J11266; JSPS KAKENHI, Grant/Award Number: 15H04642


Organisms have acquired sophisticated regulatory networks that control gene expression in response to cellular perturbations. Understanding of the mechanisms underlying the coordinated changes in gene expression in response to external and internal stimuli is a fundamental issue in biology. Recent advances in high-throughput technologies have enabled the measurement of diverse biological information, including gene expression levels, kinetics of gene expression, and interactions among gene expression regulatory molecules. By coupling these technologies with quantitative modeling, we can now uncover the biological roles and mechanisms of gene regulation at the system level. This review consists of two parts. First, we focus on the methods using uridine analogs that measure synthesis and decay rates of RNAs, which demonstrate how cells dynamically change the regulation of gene expression in response to both internal and external cues. Second, we discuss the underlying mechanisms of these changes in kinetics, including the functions of transcription factors and RNA-binding proteins. Overall, this review will help to clarify a system-level view of gene expression programs in cells.

This article is categorized under:

  • Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
  • RNA Turnover and Surveillance > Regulation of RNA Stability
  • RNA Methods > RNA Analyses in vitro and In Silico

Graphical Abstract

Transcriptional factors (TFs) regulate mRNA synthesis whereas RNA-binding proteins (RBPs) regulate mRNA fate, such as stability. Various genome-wide approaches provide the information for analyzing the function of the gene expression regulators. From these genome-wide data, computational analysis constructs gene regulatory networks.


The authors have declared no conflicts of interest for this article.