Cited by 209RNA and protein synthesis mechanismsRNA modifications and cancerGenomics and Phylogenetic Studies

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Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP

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Gogakos, Tasos, Brown, Miguel, Garzia, Aitor, Meyer, Cindy, Hafner, Markus, Tuschl, Thomas·2017·Cell Reports

DOI 10.1016/j.celrep.2017.07.029PMC PMC5564215

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Abstract

The participation of tRNAs in fundamental aspects of biology and disease necessitates an accurate, experimentally confirmed annotation of tRNA genes and curation of tRNA sequences. This has been challenging because RNA secondary structure, nucleotide modifications, and tRNA gene multiplicity complicate sequencing and mapping efforts. To address these issues, we developed hydro-tRNAseq, a method based on partial alkaline RNA hydrolysis that generates fragments amenable for sequencing. To identify transcribed tRNA genes, we further complemented this approach with photoactivatable crosslinking and immunoprecipitation (PAR-CLIP) of SSB/La, a conserved protein involved in pre-tRNA processing. Our results show that approximately half of all predicted tRNA genes are transcribed in human cells. We also report nucleotide modification sites and their order of introduction, and we identify tRNA leaders, trailers, and introns. By using complementary sequencing-based methodologies, we present a human tRNA atlas and determine expression levels of mature and processing intermediates of tRNAs in human cells.

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Authors: Gogakos, T., Brown, M., Garzia, A., Meyer, C., Hafner, M., & Tuschl, T.
Affiliations: Howard Hughes Medical Institute (US)
National Institute of Arthritis and Musculoskeletal and Skin Diseases (US)
Corresponding author: Tuschl, Thomas
ORCID: Gogakos, Tasos
Brown, Miguel
Garzia, Aitor
Meyer, Cindy
Hafner, Markus
Tuschl, Thomas
Venue: Cell Reports
Publisher: Elsevier BV
Published: 2017-08
Volume: 20
Issue: 6
Pages: 1463-1475
ISSN: 2211-1247 (ISSN-L)
DOI: 10.1016/j.celrep.2017.07.029
PMC: PMC5564215
OpenAlex: W2742715352
Cited by: 209
References: 48
Citations by year: 2026: 14 · 2025: 24 · 2024: 17 · 2023: 27 · 2022: 21 · 2021: 31 · 2020: 24 · 2019: 39 · 2018: 9 · 2017: 3
FWCI: 8.49
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by-nc-nd
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
creativecommons.org/licenses/by-nc-nd/4.0/ (vor)
Locations: Cell Reports (publishedVersion, cc-by-nc-nd)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders: NIH (TRA R01CA159227)
Weill Cornell/Rockefeller/Sloan-Kettering MD/PhD Program
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 modifications and cancer
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: tRNA, tRNA processing, PAR-CLIP, pre-tRNA processing, RNA secondary structure, nucleotide modification, tRNA introns, tRNA expression, human cells
MeSH terms: Humans, RNA Processing, Post-Transcriptional, RNA, Transfer, Sequence Analysis, RNA, HEK293 Cells

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Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP

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