Long noncoding RNA CHROMR regulates antiviral immunity in humans

Proc Natl Acad Sci U S A. 2022 Sep 13;119(37):e2210321119. doi: 10.1073/pnas.2210321119. Epub 2022 Aug 24.

Abstract

Long noncoding RNAs (lncRNAs) have emerged as critical regulators of gene expression, yet their contribution to immune regulation in humans remains poorly understood. Here, we report that the primate-specific lncRNA CHROMR is induced by influenza A virus and SARS-CoV-2 infection and coordinates the expression of interferon-stimulated genes (ISGs) that execute antiviral responses. CHROMR depletion in human macrophages reduces histone acetylation at regulatory regions of ISG loci and attenuates ISG expression in response to microbial stimuli. Mechanistically, we show that CHROMR sequesters the interferon regulatory factor (IRF)-2-dependent transcriptional corepressor IRF2BP2, thereby licensing IRF-dependent signaling and transcription of the ISG network. Consequently, CHROMR expression is essential to restrict viral infection of macrophages. Our findings identify CHROMR as a key arbitrator of antiviral innate immune signaling in humans.

Keywords: antiviral response; innate immune signaling; interferon-stimulated genes; lncRNA.

Publication types

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

MeSH terms

  • COVID-19* / genetics
  • COVID-19* / immunology
  • DNA-Binding Proteins* / metabolism
  • Humans
  • Immunity, Innate* / genetics
  • Influenza A virus* / immunology
  • Influenza, Human* / genetics
  • Influenza, Human* / immunology
  • Interferon Regulatory Factors / genetics
  • Interferon Regulatory Factors / metabolism
  • RNA, Long Noncoding* / genetics
  • RNA, Long Noncoding* / physiology
  • SARS-CoV-2* / immunology
  • Transcription Factors* / metabolism

Substances

  • DNA-Binding Proteins
  • IRF2BP2 protein, human
  • Interferon Regulatory Factors
  • RNA, Long Noncoding
  • Transcription Factors