Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques
Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and are pivotal mediators of the immune response, yet little is known about their properties at the single-cell level. Here, we generate a multi-tissue bulk RNAseq dataset from Ebola virus (EBOV) infected and not-infected r...
| Autores: | , , , , , , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2023 |
| País: | España |
| Institución: | Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya) |
| Repositorio: | Recercat. Dipósit de la Recerca de Catalunya |
| OAI Identifier: | oai:recercat.cat:10230/58199 |
| Acceso en línea: | http://hdl.handle.net/10230/58199 http://dx.doi.org/10.1038/s41467-023-39627-7 |
| Access Level: | acceso abierto |
| Palabra clave: | Ebola virus Gene regulation Genetics Rhesus macaque Transcriptomics |
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Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaquesSantus, LuisaSopena Rios, MariaGarcía Pérez, Raquel, 1989-Lin, Aaron E.Adams, Gordon C.Barnes, Kayla G.Siddle, Katherine J.Wohl, ShirleeReverter Comes, FerranRinn, John L.Bennett, Richard S.Hensley, Lisa E.Sabeti, Pardis C.Melé Messeguer, Marta, 1982-Ebola virusGene regulationGeneticsRhesus macaqueTranscriptomicsLong non-coding RNAs (lncRNAs) are involved in numerous biological processes and are pivotal mediators of the immune response, yet little is known about their properties at the single-cell level. Here, we generate a multi-tissue bulk RNAseq dataset from Ebola virus (EBOV) infected and not-infected rhesus macaques and identified 3979 novel lncRNAs. To profile lncRNA expression dynamics in immune circulating single-cells during EBOV infection, we design a metric, Upsilon, to estimate cell-type specificity. Our analysis reveals that lncRNAs are expressed in fewer cells than protein-coding genes, but they are not expressed at lower levels nor are they more cell-type specific when expressed in the same number of cells. In addition, we observe that lncRNAs exhibit similar changes in expression patterns to those of protein-coding genes during EBOV infection, and are often co-expressed with known immune regulators. A few lncRNAs change expression specifically upon EBOV entry in the cell. This study sheds light on the differential features of lncRNAs and protein-coding genes and paves the way for future single-cell lncRNA studies.This material was based upon work supported by Grant RYC-2017-22249 funded by MCIN/AEI/10.13039/501100011033 and Grant PID2019-107937GA-I00 funded by MCIN/AEI/10.13039/501100011033 (M.M.), the Howard Hughes Medical Institute Investigator Award (P.C.S.), the National Institute of Allergy and Infectious Diseases (NIAID) U19AI110818, the US Food and Drug Administration (FDA) contract HHSF223201810172C.Nature Research202320232023info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/58199http://dx.doi.org/10.1038/s41467-023-39627-7reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésNat Commun. 2023 Jun 30;14(1):3866info:eu-repo/grantAgreement/ES/2PE/PID2019-107937GA-I00© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/581992026-05-29T05:05:01Z |
| dc.title.none.fl_str_mv |
Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques |
| title |
Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques |
| spellingShingle |
Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques Santus, Luisa Ebola virus Gene regulation Genetics Rhesus macaque Transcriptomics |
| title_short |
Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques |
| title_full |
Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques |
| title_fullStr |
Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques |
| title_full_unstemmed |
Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques |
| title_sort |
Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques |
| dc.creator.none.fl_str_mv |
Santus, Luisa Sopena Rios, Maria García Pérez, Raquel, 1989- Lin, Aaron E. Adams, Gordon C. Barnes, Kayla G. Siddle, Katherine J. Wohl, Shirlee Reverter Comes, Ferran Rinn, John L. Bennett, Richard S. Hensley, Lisa E. Sabeti, Pardis C. Melé Messeguer, Marta, 1982- |
| author |
Santus, Luisa |
| author_facet |
Santus, Luisa Sopena Rios, Maria García Pérez, Raquel, 1989- Lin, Aaron E. Adams, Gordon C. Barnes, Kayla G. Siddle, Katherine J. Wohl, Shirlee Reverter Comes, Ferran Rinn, John L. Bennett, Richard S. Hensley, Lisa E. Sabeti, Pardis C. Melé Messeguer, Marta, 1982- |
| author_role |
author |
| author2 |
Sopena Rios, Maria García Pérez, Raquel, 1989- Lin, Aaron E. Adams, Gordon C. Barnes, Kayla G. Siddle, Katherine J. Wohl, Shirlee Reverter Comes, Ferran Rinn, John L. Bennett, Richard S. Hensley, Lisa E. Sabeti, Pardis C. Melé Messeguer, Marta, 1982- |
| author2_role |
author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
Ebola virus Gene regulation Genetics Rhesus macaque Transcriptomics |
| topic |
Ebola virus Gene regulation Genetics Rhesus macaque Transcriptomics |
| description |
Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and are pivotal mediators of the immune response, yet little is known about their properties at the single-cell level. Here, we generate a multi-tissue bulk RNAseq dataset from Ebola virus (EBOV) infected and not-infected rhesus macaques and identified 3979 novel lncRNAs. To profile lncRNA expression dynamics in immune circulating single-cells during EBOV infection, we design a metric, Upsilon, to estimate cell-type specificity. Our analysis reveals that lncRNAs are expressed in fewer cells than protein-coding genes, but they are not expressed at lower levels nor are they more cell-type specific when expressed in the same number of cells. In addition, we observe that lncRNAs exhibit similar changes in expression patterns to those of protein-coding genes during EBOV infection, and are often co-expressed with known immune regulators. A few lncRNAs change expression specifically upon EBOV entry in the cell. This study sheds light on the differential features of lncRNAs and protein-coding genes and paves the way for future single-cell lncRNA studies. |
| publishDate |
2023 |
| dc.date.none.fl_str_mv |
2023 2023 2023 |
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info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
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article |
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publishedVersion |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10230/58199 http://dx.doi.org/10.1038/s41467-023-39627-7 |
| url |
http://hdl.handle.net/10230/58199 http://dx.doi.org/10.1038/s41467-023-39627-7 |
| dc.language.none.fl_str_mv |
Inglés |
| language_invalid_str_mv |
Inglés |
| dc.relation.none.fl_str_mv |
Nat Commun. 2023 Jun 30;14(1):3866 info:eu-repo/grantAgreement/ES/2PE/PID2019-107937GA-I00 |
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http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess |
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http://creativecommons.org/licenses/by/4.0/ |
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openAccess |
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application/pdf application/pdf |
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Nature Research |
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Nature Research |
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reponame:Recercat. Dipósit de la Recerca de Catalunya instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya) |
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Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya) |
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Recercat. Dipósit de la Recerca de Catalunya |
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