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

Characterizing expression and processing of precursor and mature human tRNAs by hydro-tRNAseq and PAR-CLIP

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

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.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.celrep.2017.07.029

Cites

48 of 48 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 1

  1. Hafner M Renwick N Farazi TA Mihailović A Pena JTG Tuschl T 2012b Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing Methods 58 164 170 22885844 PMC3508525

Cited by

Sorted by citations

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
Venue
Cell Reports
Publisher
Elsevier BV
Published
2017-08
Volume
20
Issue
6
Pages
1463-1475
ISSN
2211-1247 (ISSN-L)
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
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review