Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome
Resumen:
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.
2020 | |
Inglés | |
Universidad de la República | |
COLIBRI | |
https://hdl.handle.net/20.500.12008/31657 | |
Acceso abierto | |
Licencia Creative Commons Atribución (CC - By 4.0) |
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---|---|
author | Tosar Rovira, Juan Pablo |
author2 | Segovia, Mercedes Castellano, Mauricio Gámbaro, Fabiana Akiyama, Y. Olivera, Álvaro Costa Camacho, Bruno Alejo Possi, Tania Hill, Marcelo Ivanov, Pavel Cayota, Alfonso |
author2_role | author author author author author author author author author author |
author_facet | Tosar Rovira, Juan Pablo Segovia, Mercedes Castellano, Mauricio Gámbaro, Fabiana Akiyama, Y. Olivera, Álvaro Costa Camacho, Bruno Alejo Possi, Tania Hill, Marcelo Ivanov, Pavel Cayota, Alfonso |
author_role | author |
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collection | COLIBRI |
dc.contributor.filiacion.none.fl_str_mv | Tosar Rovira Juan Pablo, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Investigaciones Nucleares Segovia Mercedes, Instituto Pasteur (Montevideo) Castellano Mauricio, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Investigaciones Nucleares Gámbaro Fabiana, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Investigaciones Nucleares Akiyama Y. Olivera Álvaro, Universidad de la República (Uruguay). CURE Costa Camacho Bruno Alejo, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Investigaciones Nucleares Possi Tania, Instituto Pasteur (Montevideo) Hill Marcelo, Instituto Pasteur (Montevideo) Ivanov Pavel Cayota Alfonso, Instituto Pasteur (Montevideo) |
dc.creator.none.fl_str_mv | Tosar Rovira, Juan Pablo Segovia, Mercedes Castellano, Mauricio Gámbaro, Fabiana Akiyama, Y. Olivera, Álvaro Costa Camacho, Bruno Alejo Possi, Tania Hill, Marcelo Ivanov, Pavel Cayota, Alfonso |
dc.date.accessioned.none.fl_str_mv | 2022-05-25T13:27:30Z |
dc.date.available.none.fl_str_mv | 2022-05-25T13:27:30Z |
dc.date.issued.none.fl_str_mv | 2020 |
dc.description.abstract.none.fl_txt_mv | 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. |
dc.format.extent.es.fl_str_mv | 15 h. |
dc.format.mimetype.es.fl_str_mv | application/pdf |
dc.identifier.citation.es.fl_str_mv | Tosar Rovira, J, Segovia, M, Castellano, M, [y otros] "Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome". Nucleic Acids Research. [en línea] 2020, 48(22): 12874–12888. DOI: 10.1093/nar/gkaa674 |
dc.identifier.doi.none.fl_str_mv | 10.1093/nar/gkaa674 |
dc.identifier.issn.none.fl_str_mv | 1362-4962 |
dc.identifier.uri.none.fl_str_mv | https://hdl.handle.net/20.500.12008/31657 |
dc.language.iso.none.fl_str_mv | en eng |
dc.publisher.es.fl_str_mv | Oxford University Press |
dc.relation.ispartof.es.fl_str_mv | Nucleic Acids Research, 2020, 48(22): 12874–12888 |
dc.rights.license.none.fl_str_mv | Licencia Creative Commons Atribución (CC - By 4.0) |
dc.rights.none.fl_str_mv | info:eu-repo/semantics/openAccess |
dc.source.none.fl_str_mv | reponame:COLIBRI instname:Universidad de la República instacron:Universidad de la República |
dc.title.none.fl_str_mv | Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome |
dc.type.es.fl_str_mv | Artículo |
dc.type.none.fl_str_mv | info:eu-repo/semantics/article |
dc.type.version.none.fl_str_mv | info:eu-repo/semantics/publishedVersion |
description | 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. |
eu_rights_str_mv | openAccess |
format | article |
id | COLIBRI_a7a9f539e22cb7bc3ad8fb9a901e3332 |
identifier_str_mv | Tosar Rovira, J, Segovia, M, Castellano, M, [y otros] "Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome". Nucleic Acids Research. [en línea] 2020, 48(22): 12874–12888. DOI: 10.1093/nar/gkaa674 1362-4962 10.1093/nar/gkaa674 |
instacron_str | Universidad de la República |
institution | Universidad de la República |
instname_str | Universidad de la República |
language | eng |
language_invalid_str_mv | en |
network_acronym_str | COLIBRI |
network_name_str | COLIBRI |
oai_identifier_str | oai:colibri.udelar.edu.uy:20.500.12008/31657 |
publishDate | 2020 |
reponame_str | COLIBRI |
repository.mail.fl_str_mv | mabel.seroubian@seciu.edu.uy |
repository.name.fl_str_mv | COLIBRI - Universidad de la República |
repository_id_str | 4771 |
rights_invalid_str_mv | Licencia Creative Commons Atribución (CC - By 4.0) |
spelling | Tosar Rovira Juan Pablo, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Investigaciones NuclearesSegovia Mercedes, Instituto Pasteur (Montevideo)Castellano Mauricio, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Investigaciones NuclearesGámbaro Fabiana, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Investigaciones NuclearesAkiyama Y.Olivera Álvaro, Universidad de la República (Uruguay). CURECosta Camacho Bruno Alejo, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Investigaciones NuclearesPossi Tania, Instituto Pasteur (Montevideo)Hill Marcelo, Instituto Pasteur (Montevideo)Ivanov PavelCayota Alfonso, Instituto Pasteur (Montevideo)2022-05-25T13:27:30Z2022-05-25T13:27:30Z2020Tosar Rovira, J, Segovia, M, Castellano, M, [y otros] "Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome". Nucleic Acids Research. [en línea] 2020, 48(22): 12874–12888. DOI: 10.1093/nar/gkaa6741362-4962https://hdl.handle.net/20.500.12008/3165710.1093/nar/gkaa674A 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.Submitted by Verdun Juan Pablo (jverdun@fcien.edu.uy) on 2022-05-24T22:42:02Z No. of bitstreams: 2 license_rdf: 19875 bytes, checksum: 9fdbed07f52437945402c4e70fa4773e (MD5) 10.1093nargkaa674.pdf: 4462118 bytes, checksum: 6347a5689f6767b54067f7f23cdb7105 (MD5)Approved for entry into archive by Faget Cecilia (lfaget@fcien.edu.uy) on 2022-05-25T13:11:03Z (GMT) No. of bitstreams: 2 license_rdf: 19875 bytes, checksum: 9fdbed07f52437945402c4e70fa4773e (MD5) 10.1093nargkaa674.pdf: 4462118 bytes, checksum: 6347a5689f6767b54067f7f23cdb7105 (MD5)Made available in DSpace by Luna Fabiana (fabiana.luna@seciu.edu.uy) on 2022-05-25T13:27:30Z (GMT). No. of bitstreams: 2 license_rdf: 19875 bytes, checksum: 9fdbed07f52437945402c4e70fa4773e (MD5) 10.1093nargkaa674.pdf: 4462118 bytes, checksum: 6347a5689f6767b54067f7f23cdb7105 (MD5) Previous issue date: 202015 h.application/pdfenengOxford University PressNucleic Acids Research, 2020, 48(22): 12874–12888Las obras depositadas en el Repositorio se rigen por la Ordenanza de los Derechos de la Propiedad Intelectual de la Universidad de la República.(Res. Nº 91 de C.D.C. de 8/III/1994 – D.O. 7/IV/1994) y por la Ordenanza del Repositorio Abierto de la Universidad de la República (Res. 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- Universidad de la Repúblicafalse |
spellingShingle | Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome Tosar Rovira, Juan Pablo |
status_str | publishedVersion |
title | Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome |
title_full | Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome |
title_fullStr | Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome |
title_full_unstemmed | Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome |
title_short | Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome |
title_sort | Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome |
url | https://hdl.handle.net/20.500.12008/31657 |