Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques

Luisa Santus, Maria Sopena-Rios, Raquel García-Pérez, Aaron E. Lin, Gordon C. Adams, Kayla G. Barnes, Katherine J. Siddle, Shirlee Wohl, Ferran Reverter, John L. Rinn, Richard S. Bennett, Lisa E. Hensley (), Pardis C. Sabeti () and Marta Melé ()
Additional contact information
Luisa Santus: Barcelona Supercomputing Center
Maria Sopena-Rios: Barcelona Supercomputing Center
Raquel García-Pérez: Barcelona Supercomputing Center
Aaron E. Lin: Harvard University
Gordon C. Adams: Harvard University
Kayla G. Barnes: Broad Institute of MIT and Harvard
Katherine J. Siddle: Harvard University
Shirlee Wohl: Harvard University
Ferran Reverter: Microbiology and Statistics University of Barcelona
John L. Rinn: University of Colorado Boulder
Richard S. Bennett: National Institutes of Health
Lisa E. Hensley: National Institutes of Health
Pardis C. Sabeti: Harvard University
Marta Melé: Barcelona Supercomputing Center

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: Abstract 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.

Date: 2023
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-023-39627-7 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39627-7

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-023-39627-7

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().