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A standardized ontology for naming tRNA-derived RNAs based on molecular origin

Nature Methods (2023)Cite this article

Subjects

The tDR naming system (Fig. 1a) consists of three required components, plus up to two supplemental notations in special cases. First, each name starts with the general prefix “tDR,” which is neutral to any functional role. If the tDR is derived from mitochondrial or plastid tRNAs, “mtDR” or “ptDR” is used. Second, the tDR’s precise start and end positions, relative to its source tRNA, are specified using the standardized Sprinzl tRNA position numbering10 (for example, “tDR-4:33”). This system gives stems and loops consistent base numbers across all tRNAs (for example, the anticodon in every tRNA is at positions 34–36). Third, the identifier of the most similar source tRNA found in the Genomic tRNA Database (GtRNAdb)9 is appended to the tDR name (for example, “Val-AAC-1”). Because some portions of different tRNAs may be identical, tDRs can often be derived from multiple indistinguishable parent tRNAs. In this case, a fourth component is added to the tDR name to indicate the number of potential source tRNAs (for example, “M7”). Finally, nucleotide differences may exist between tDRs and the reference tRNA set as a result of natural genetic variation, or may also be caused by misincorporation by reverse transcriptase at certain RNA modifications. To describe these tDRs succinctly, a name component can be added consisting of the original and substituted bases with their relative positions (for example, “U10A”).

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Fig. 1: Standardized naming for tRNA-derived RNAs (tDRs) illustrated by seven tDRs potentially derived from up to eight human tRNAPro transcripts.

Data availability

The tDRnamer web server is available at http://trna.ucsc.edu/tDRnamer/. Standalone software can be obtained from GitHub at https://github.com/UCSC-LoweLab/tDRnamer and a Docker image at https://hub.docker.com/r/ucsclowelab/tdrnamer. Example data can be downloaded from http://trna.ucsc.edu/tDRnamer/data/examples/. Prebuilt reference databases for model organisms are available at http://trna.ucsc.edu/tDRnamer/docs/refdb/. The complete set of tRFdb3 data reannotations by tDRnamer is available at http://trna.ucsc.edu/tDRnamer/data/tRFdb_reannotations/.

Code availability

The source code of tDRnamer and the source code of its web server are available at https://github.com/UCSC-LoweLab/tDRnamer and https://github.com/UCSC-LoweLab/tDRnamer-web, respectively, both under the GNU General Public License v3.0.

References

  1. Cozen, A. E. et al. Nat. Methods 12, 879–884 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Shi, J. et al. Nat. Cell Biol. 23, 424–436 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Kumar, P., Mudunuri, S. B., Anaya, J. & Dutta, A. Nucleic Acids Res. 43, D141–D145 (2015).

    Article  CAS  PubMed  Google Scholar 

  4. Gebetsberger, J. & Polacek, N. RNA Biol. 10, 1798–1806 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Polacek, N. & Ivanov, P. RNA Biol. 17, 1057–1059 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Kim, H. K., Yeom, J. H. & Kay, M. A. Mol. Ther. 28, 2340–2357 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Magee, R. & Rigoutsos, I. Nucleic Acids Res. 48, 9433–9448 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Pliatsika, V. et al. Nucleic Acids Res. 46 (D1), D152–D159 (2018).

  9. Chan, P. P. & Lowe, T. M. Nucleic Acids Res. 44 (D1), D184–D189 (2016).

  10. Steinberg, S., Misch, A. & Sprinzl, M. Nucleic Acids Res. 21, 3011–3015 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Human Genome Research Institute, National Institutes of Health (R01HG006753 to T.L.).

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Author notes

  1. These authors contributed equally: Andrew D. Holmes, Patricia P. Chan.

Authors and Affiliations

  1. Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA

    Andrew D. Holmes, Patricia P. Chan & Todd M. Lowe

  2. Division of Urology, Department of Surgery, School of Medicine, University of Utah, Salt Lake City, UT, USA

    Qi Chen

  3. Department of Medicine, Harvard Medical School, Boston, MA, USA

    Pavel Ivanov

  4. Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, Strasbourg, France

    Laurence Drouard

  5. Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland

    Norbert Polacek

  6. Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USA

    Mark A. Kay

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Contributions

A.H. and P.C. designed and developed tDRnamer standalone software. P.C. designed and developed the tDRnamer web server. P.C. and T.L. wrote the manuscript. All authors contributed to the design of tDR naming convention and the feature requirements of tDRnamer.

Corresponding author

Correspondence to Todd M. Lowe.

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The authors declare no competing interests.

Peer review

Peer review information

Nature Methods thanks Hani Goodarzi and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Supplementary information

Supplementary Information

Supplementary Figs. 1–3, Tables 1–4 and Methods

Supplementary Data 1

Reannotation of human tRNA-derived RNAs in tRFdb using tDRnamer

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Holmes, A.D., Chan, P.P., Chen, Q. et al. A standardized ontology for naming tRNA-derived RNAs based on molecular origin. Nat Methods (2023). https://doi.org/10.1038/s41592-023-01813-2

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