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

• Published in: Nature communications 2023-06, Vol.14 (1), p.3866-14, Article 3866
• Main Authors: Santus, Luisa, Sopena-Rios, Maria, García-Pérez, Raquel, Lin, Aaron E., Adams, Gordon C., Barnes, Kayla G., Siddle, Katherine J., Wohl, Shirlee, Reverter, Ferran, Rinn, John L., Bennett, Richard S., Hensley, Lisa E., Sabeti, Pardis C., Melé, Marta
• Format: Article
• Language: English
• Subjects: 38/39; 45/91; 631/1647/334/1874/1625; 631/208; 631/208/200; 631/208/212/2019; 631/326/596/2042; Animals; Biological activity; Coding; Ebola virus; Ebolavirus; Ebolavirus - genetics; Genes; Hemorrhagic Fever, Ebola - genetics; Humanities and Social Sciences; Immune response; Immune system; Infections; Macaca mulatta; multidisciplinary; Non-coding RNA; Proteins; RNA, Long Noncoding - genetics; Science; Science (multidisciplinary); Viral diseases; Virus Internalization
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-39627-7

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. Long non-coding RNAs (lncRNAs) play key roles in the immune response but their properties at the single-cell level are less well understood. Here, the authors characterize differential features of lncRNAs and protein-coding genes upon Ebola infection in macaques at single-cell resolution.