Advanced Review
Contributions of regulated transcription and mRNA decay to the dynamics of gene expression
Toshimichi Yamada,
Nobuyoshi Akimitsu,
Toshimichi Yamada
Department of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Tokyo, Japan
Search for more papers by this authorCorresponding Author
Nobuyoshi Akimitsu
Isotope Science Center, University of Tokyo, Tokyo, Japan
Correspondence
Nobuyoshi Akimitsu, Isotope Science Center, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
Email: [email protected]
Search for more papers by this authorToshimichi Yamada,
Nobuyoshi Akimitsu,
Toshimichi Yamada
Department of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Tokyo, Japan
Search for more papers by this authorCorresponding Author
Nobuyoshi Akimitsu
Isotope Science Center, University of Tokyo, Tokyo, Japan
Correspondence
Nobuyoshi Akimitsu, Isotope Science Center, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
Email: [email protected]
Search for more papers by this authorFunding information JSPS Research Fellows, Grant/Award Number: 17J11266; JSPS KAKENHI, Grant/Award Number: 15H04642
Abstract
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.
CONFLICT OF INTEREST
The authors have declared no conflicts of interest for this article.
Supporting Information
| Filename | Description |
|---|---|
| wrna1508-sup-0001-Table.pdfPDF document, 3 MB | Table S1 List of RNA-binding transcription factors. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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