Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates
- Kentaro Kawata1,
- Hiroyasu Wakida2,
- Toshimichi Yamada3,
- Kenzui Taniue1,
- Han Han2,
- Masahide Seki4,
- Yutaka Suzuki4 and
- Nobuyoshi Akimitsu1
- 1Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan;
- 2Department of Pharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan;
- 3Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Tokyo 204-0004, Japan;
- 4Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
Abstract
Gene expression is determined by a balance between RNA synthesis and RNA degradation. To elucidate the underlying regulatory mechanisms and principles of this, simultaneous measurements of RNA synthesis and degradation are required. Here, we report the development of “Dyrec-seq,” which uses 4-thiouridine and 5-bromouridine to simultaneously quantify RNA synthesis and degradation rates. Dyrec-seq enabled the quantification of RNA synthesis and degradation rates of 4702 genes in HeLa cells. Functional enrichment analysis showed that the RNA synthesis and degradation rates of genes are actually determined by the genes’ biological functions. A comparison of theoretical and experimental analyses revealed that the amount of RNA is determined by the ratio of RNA synthesis to degradation rates, whereas the rapidity of responses to external stimuli is determined only by the degradation rate. This study emphasizes that not only RNA synthesis but also RNA degradation is important in shaping gene expression patterns.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.264408.120.
- Received April 7, 2020.
- Accepted August 20, 2020.
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