Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
16 12 2020
16 12 2020
Historique:
accepted:
31
07
2020
revised:
19
07
2020
received:
18
04
2020
pubmed:
14
8
2020
medline:
15
1
2021
entrez:
14
8
2020
Statut:
ppublish
Résumé
A major proportion of extracellular RNAs (exRNAs) do not copurify with extracellular vesicles (EVs) and remain in ultracentrifugation supernatants of cell-conditioned medium or mammalian blood serum. However, little is known about exRNAs beyond EVs. We have previously shown that the composition of the nonvesicular exRNA fraction is highly biased toward specific tRNA-derived fragments capable of forming RNase-protecting dimers. To solve the problem of stability in exRNA analysis, we developed a method based on sequencing the size exclusion chromatography (SEC) fractions of nonvesicular extracellular samples treated with RNase inhibitors (RI). This method revealed dramatic compositional changes in exRNA population when enzymatic RNA degradation was inhibited. We demonstrated the presence of ribosomes and full-length tRNAs in cell-conditioned medium of a variety of mammalian cell lines. Their fragmentation generates some small RNAs that are highly resistant to degradation. The extracellular biogenesis of some of the most abundant exRNAs demonstrates that extracellular abundance is not a reliable input to estimate RNA secretion rates. Finally, we showed that chromatographic fractions containing extracellular ribosomes are probably not silent from an immunological perspective and could possibly be decoded as damage-associated molecular patterns.
Identifiants
pubmed: 32785615
pii: 5891565
doi: 10.1093/nar/gkaa674
pmc: PMC7736827
doi:
Substances chimiques
Culture Media, Conditioned
0
Enzyme Inhibitors
0
RNA
63231-63-0
RNA, Transfer
9014-25-9
Ribonucleases
EC 3.1.-
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
12874-12888Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM126150
Pays : United States
Organisme : NCI NIH HHS
ID : UG3 CA241694
Pays : United States
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
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