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

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-

doi:http://dx.doi.org/10.1038/s41467-023-39627-7

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

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Santus L, Sopena-Rios M, García-Pérez R, Lin AE, Adams GC, Barnes KG, Siddle KJ, Wohl S, Reverter F, Rinn JL, Bennett RS, Hensley LE, Sabeti PC, Melé M. Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques. Nat Commun. 2023 Jun 30;14(1):3866. DOI: 10.1038/s41467-023-39627-7

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.