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Quantification of substoichiometric modification reveals global.....pdf (12.87 MB)

Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines

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posted on 2023-01-25, 17:13 authored by Florian Pichot, Marion Hogg, Virginie Marchand, Valérie Bourguignon, Elisabeth JirströmElisabeth Jirström, Cliona Farrell, Hesham Gibriel, Jochen PrehnJochen Prehn, Yuri Motorin, Mark Helm

Modification of tRNA is an integral part of the epitranscriptome with a particularly pronounced potential to generate diversity in RNA expression. Eukaryotic tRNA contains modifications in up to 20% of their nucleotides, but not all sites are always fully modified. Combinations and permutations of partially modified sites in tRNAs can generate a plethora of tRNA isoforms, termed modivariants. Here, we investigate the stoichiometry of incompletely modified sites in tRNAs from human cell lines for their information content. Using a panel of RNA modification mapping methods, we assess the stoichiometry of sites that contain the modifications 5-methylcytidine (m5C), 2'-O-ribose methylation (Nm), 3-methylcytidine (m3C), 7-methylguanosine (m7G), and Dihydrouridine (D). We discovered that up to 75% of sites can be incompletely modified and that the differential modification status of a cellular tRNA population holds information that allows to discriminate e.g. different cell lines. As a further aspect, we investigated potential causal connectivity between tRNA modification and its processing into tRNA fragments (tiRNAs and tRFs). Upon exposure of cultured living cells to cell-penetrating angiogenin, the modification patterns of the corresponding RNA populations was changed. Importantly, we also found that tsRNAs were significantly less modified than their parent tRNAs at numerous sites, suggesting that tsRNAs might derive chiefly from hypomodified tRNAs. 

Funding

Science Foundation Ireland (SFI) under Grant Number 16/RC/3948

European Regional Development Fund

StAR International PhD Scholarship from the Royal College of Surgeons in Ireland

Joint Programme in Neurodegeneration Research (JPND) project RNA-NEURO (Bmbf FKZ: 01ED1804)

Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project-ID 439669440 – TRR 319 (C01)

Project HE 3397/21-1

Joint Programme in Neurodegeneration Research (JPND) project RNA-NEURO (17/JPND/3455)

FutureNeuro industry partners

History

Comments

The original article is available at https://www.sciencedirect.com/

Published Citation

Pichot F. Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines. Comput Struct Biotechnol J. 2022;21:401-417.

Publication Date

19 December 2022

PubMed ID

36618980

Department/Unit

  • Physiology and Medical Physics
  • FutureNeuro Centre

Publisher

Elsevier

Version

  • Published Version (Version of Record)