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

Author

Listed:
  • Luisa Santus

    (Barcelona Supercomputing Center
    The Barcelona Institute for Science and Technology)

  • Maria Sopena-Rios

    (Barcelona Supercomputing Center)

  • Raquel García-Pérez

    (Barcelona Supercomputing Center)

  • Aaron E. Lin

    (Harvard University
    Broad Institute of MIT and Harvard
    Harvard Medical School)

  • Gordon C. Adams

    (Harvard University
    Broad Institute of MIT and Harvard)

  • Kayla G. Barnes

    (Broad Institute of MIT and Harvard
    Harvard University
    Liverpool School of Tropical Medicine)

  • Katherine J. Siddle

    (Harvard University
    Broad Institute of MIT and Harvard)

  • Shirlee Wohl

    (Harvard University
    Broad Institute of MIT and Harvard
    The Scripps Research Institute, Department of Immunology and Microbiology)

  • 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
    Broad Institute of MIT and Harvard
    Harvard Medical School
    Howard Hughes Medical Institute)

  • Marta Melé

    (Barcelona Supercomputing Center)

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.

Suggested Citation

  • 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 & L, 2023. "Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39627-7
    DOI: 10.1038/s41467-023-39627-7
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    References listed on IDEAS

    as
    1. Anamaria Necsulea & Magali Soumillon & Maria Warnefors & Angélica Liechti & Tasman Daish & Ulrich Zeller & Julie C. Baker & Frank Grützner & Henrik Kaessmann, 2014. "The evolution of lncRNA repertoires and expression patterns in tetrapods," Nature, Nature, vol. 505(7485), pages 635-640, January.
    2. Orit Rozenblatt-Rosen & Michael J. T. Stubbington & Aviv Regev & Sarah A. Teichmann, 2017. "The Human Cell Atlas: from vision to reality," Nature, Nature, vol. 550(7677), pages 451-453, October.
    3. Adam T. Waickman & Kaitlin Victor & Tao Li & Kristin Hatch & Wiriya Rutvisuttinunt & Carey Medin & Benjamin Gabriel & Richard G. Jarman & Heather Friberg & Jeffrey R. Currier, 2019. "Dissecting the heterogeneity of DENV vaccine-elicited cellular immunity using single-cell RNA sequencing and metabolic profiling," Nature Communications, Nature, vol. 10(1), pages 1-16, December.
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