Expression of novel long noncoding RNAs defines virus-specific effector and memory CD8+ T cells

Nat Commun. 2019 Jan 14;10(1):196. doi: 10.1038/s41467-018-07956-7.


In response to viral infection, CD8+ T cells undergo expansion and differentiate into distinct classes of effector cells. After clearance of the virus, a small population of long-lived memory cells persists. Comprehensive studies have defined the protein-coding transcriptional changes associated with this process. Here we expand on this prior work by performing RNA-sequencing to identify changes in long noncoding RNA (lncRNA) expression in human and mouse CD8+ T cells responding to viral infection. We identify hundreds of unannotated lncRNAs and show that expression profiles of both known and novel lncRNAs are sufficient to define naive, effector, and memory CD8+ T cell subsets, implying that they may be involved in fate decisions during antigen-driven differentiation. Additionally, in comparing mouse and human lncRNA expression, we find that lncRNAs with conserved sequence undergo similar changes in expression in the two species, suggesting an evolutionarily conserved role for lncRNAs during CD8+ T cell differentiation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • CD8-Positive T-Lymphocytes / immunology*
  • CD8-Positive T-Lymphocytes / metabolism
  • Cell Differentiation / genetics*
  • Cell Differentiation / immunology
  • Conserved Sequence / genetics
  • Conserved Sequence / immunology
  • Datasets as Topic
  • Disease Models, Animal
  • Gene Expression Profiling
  • Humans
  • Immunologic Memory / genetics
  • Lymphocyte Activation / genetics
  • Lymphocytic Choriomeningitis / immunology*
  • Lymphocytic Choriomeningitis / virology
  • Lymphocytic choriomeningitis virus / immunology
  • Mice
  • Mice, Inbred C57BL
  • RNA, Long Noncoding / immunology
  • RNA, Long Noncoding / isolation & purification
  • RNA, Long Noncoding / metabolism*
  • Sequence Analysis, RNA
  • Synteny / immunology
  • T-Lymphocyte Subsets / immunology*
  • T-Lymphocyte Subsets / metabolism
  • Transcriptome / immunology


  • RNA, Long Noncoding