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Nucleic acids research
11 04, 2020;48 (19): 10890-10908.

HIV-1 infection activates endogenous retroviral promoters regulating antiviral gene expression.

Smitha Srinivasachar Badarinarayan, Irina Shcherbakova, Simon Langer, Lennart Koepke, Andrea Preising, Dominik Hotter, Frank Kirchhoff, Konstantin M J Sparrer, Gunnar Schotta, Daniel Sauter
Author Information
  1. Smitha Srinivasachar Badarinarayan: Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.
  2. Irina Shcherbakova: Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany.
  3. Simon Langer: Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.
  4. Lennart Koepke: Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.
  5. Andrea Preising: Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.
  6. Dominik Hotter: Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.
  7. Frank Kirchhoff: Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.
  8. Konstantin M J Sparrer: Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.
  9. Gunnar Schotta: Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany.
  10. Daniel Sauter: Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.
PMID: 33021676 DOI: 10.1093/nar/gkaa832

Abstract

Although endogenous retroviruses (ERVs) are known to harbor cis-regulatory elements, their role in modulating cellular immune responses remains poorly understood. Using an RNA-seq approach, we show that several members of the ERV9 lineage, particularly LTR12C elements, are activated upon HIV-1 infection of primary CD4+ T cells. Intriguingly, HIV-1-induced ERVs harboring transcription start sites are primarily found in the vicinity of immunity genes. For example, HIV-1 infection activates LTR12C elements upstream of the interferon-inducible genes GBP2 and GBP5 that encode for broad-spectrum antiviral factors. Reporter assays demonstrated that these LTR12C elements drive gene expression in primary CD4+ T cells. In line with this, HIV-1 infection triggered the expression of a unique GBP2 transcript variant by activating a cryptic transcription start site within LTR12C. Furthermore, stimulation with HIV-1-induced cytokines increased GBP2 and GBP5 expression in human cells, but not in macaque cells that naturally lack the GBP5 gene and the LTR12C element upstream of GBP2. Finally, our findings suggest that GBP2 and GBP5 have already been active against ancient viral pathogens as they suppress the maturation of the extinct retrovirus HERV-K (HML-2). In summary, our findings uncover how human cells can exploit remnants of once-infectious retroviruses to regulate antiviral gene expression.

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MeSH Term

Animals
CD4-Positive T-Lymphocytes
Endogenous Retroviruses
GTP-Binding Proteins
Gene Expression Regulation
HEK293 Cells
HIV Infections
HIV-1
Humans
Macaca mulatta
Promoter Regions, Genetic
T-Lymphocyte Subsets

Chemicals

GBP5 protein, human
GBP2 protein, human
GTP-Binding Proteins
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 12

Word Cloud

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