Simultaneous measurement of nascent transcriptome and translatome using 4-thiouridine metabolic RNA labeling and translating ribosome affinity purification
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Abstract
Regulation of gene expression in response to various biological processes, including extracellular stimulation and environmental adaptation requires nascent RNA synthesis and translation. Analysis of the coordinated regulation of dynamic RNA synthesis and translation is required to determine functional protein production. However, reliable methods for the simultaneous measurement of nascent RNA synthesis and translation at the gene level are limited. Here, we developed a novel method for the simultaneous assessment of nascent RNA synthesis and translation by combining 4-thiouridine (4sU) metabolic RNA labeling and translating ribosome affinity purification (TRAP) using a monoclonal antibody against evolutionarily conserved ribosomal P-stalk proteins. The P-stalk-mediated TRAP (P-TRAP) technique recovered endogenous translating ribosomes, allowing easy translatome analysis of various eukaryotes. We validated this method in mammalian cells by demonstrating that acute unfolded protein response (UPR) in the endoplasmic reticulum (ER) induces dynamic reprogramming of nascent RNA synthesis and translation. Our nascent P-TRAP (nP-TRAP) method may serve as a simple and powerful tool for analyzing the coordinated regulation of transcription and translation of individual genes in various eukaryotes.
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Cites
Global quantification of mammalian gene expression control
Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · cited 2× · see citing works
“13 reflecting a low correlation between the transcriptome characterized by standard RNA328 seq and the translatome (4,19-21) both in the presence or absence of thapsigargin.”
BackgroundA translational profiling approach for the molecular characterization of CNS cell types
Heiman, M., Schaefer, A., Gong, S., Peterson, J. D., Day, M., Ramsey, K. E., Suárez-Fariñas, M., Schwarz, C., Stephan, D. A., Surmeier, D. J., et al. (2008) · Cell · doi:10.1016/j.cell.2008.10.028 · Cited by 1,134 · see citing works
Thiol-linked alkylation for the metabolic sequencing of RNA
Herzog, V. A., Reichholf, B., Neumann, T., Rescheneder, P., Bhat, P., Burkard, T. R., Wlotzka, W., von Haeseler, A., Zuber, J., & Ameres, S. L. (2017) · doi:10.1101/177642 · Cited by 622 · see citing works
Cell type–specific mRNA purification by translating ribosome affinity purification (TRAP)
Heiman, M., Kulicke, R., Fenster, R. J., Greengard, P., & Heintz, N. (2014) · Nature Protocols · doi:10.1038/nprot.2014.085 · Cited by 498 · see citing works
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- Authors
- Imai, H., Utsumi, D., Torihara, H., Takahashi, K., Kuroyanagi, H., & Yamashita, A.
- Affiliations
- University of the Ryukyus (JP)
- Corresponding author
- Imai, Hirotatsu
- Yamashita, Akio
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2023-06-28
- Volume
- 51
- Issue
- 14
- Pages
- e76-e76
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC10415123
- OpenAlex
- W4382345144
- Cited by
- 9
- References
- 4
- Citations by year
- 2026: 2 · 2025: 4 · 2024: 3
- FWCI
- 0.80
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Institutional Repositories DataBase (IRDB) (submittedVersion, cc-by)
- University oh the Ryukyus Repository (submittedVersion, cc-by-nc-nd)
- Funders
- JSPS (20J00036, 21K15015, 20H03438, 21K19413, 20H04839, 20H03181)
- Japan Science and Technology Agency (JPMJMS2022)
- Takeda Science Foundation
- Bristol Myers Squibb
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Keywords
- translatome, translating ribosome affinity purification, unfolded protein response, gene expression regulation
- MeSH terms
- Ribosome Profiling, Animals, Gene Expression Regulation, Genetic Techniques, Mammals, Ribosomes, RNA, Thiouridine, Protein Biosynthesis, Transcriptome
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