HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages

PLoS One. 2015 Jul 30;10(7):e0132127. doi: 10.1371/journal.pone.0132127. eCollection 2015.


Background: MiRNAs and other small noncoding RNAs (sncRNAs) are key players in post-transcriptional gene regulation. HIV-1 derived small noncoding RNAs (sncRNAs) have been described in HIV-1 infected cells, but their biological functions still remain to be elucidated. Here, we approached the question whether viral sncRNAs may play a role in the RNA interference (RNAi) pathway or whether viral mRNAs are targeted by cellular miRNAs in human monocyte derived macrophages (MDM).

Methods: The incorporation of viral sncRNAs and/or their target RNAs into RNA-induced silencing complex was investigated using photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) as well as high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP), which capture Argonaute2-bound miRNAs and their target RNAs. HIV-1 infected monocyte-derived macrophages (MDM) were chosen as target cells, as they have previously been shown to express HIV-1 sncRNAs. In addition, we applied small RNA deep sequencing to study differential cellular miRNA expression in HIV-1 infected versus non-infected MDMs.

Results and conclusion: PAR-CLIP and HITS-CLIP data demonstrated the absence of HIV-1 RNAs in Ago2-RISC, although the presence of a multitude of HIV-1 sncRNAs in HIV-1 infected MDMs was confirmed by small RNA sequencing. Small RNA sequencing revealed that 1.4% of all sncRNAs were of HIV-1 origin. However, neither HIV-1 derived sncRNAs nor putative HIV-1 target sequences incorporated into Ago2-RISC were identified suggesting that HIV-1 sncRNAs are not involved in the canonical RNAi pathway nor is HIV-1 targeted by this pathway in HIV-1 infected macrophages.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Argonaute Proteins / genetics*
  • Base Sequence
  • Cell Line
  • Gene Expression Regulation
  • HEK293 Cells
  • HIV-1 / genetics*
  • Humans
  • Macrophages / immunology*
  • MicroRNAs / genetics
  • RNA Interference*
  • RNA, Viral / genetics*
  • Sequence Alignment
  • Sequence Analysis, RNA


  • AGO2 protein, human
  • Argonaute Proteins
  • MicroRNAs
  • RNA, Viral

Associated data

  • GEO/GSE70851

Grants and funding

This study was funded by the Swiss National Science Foundation (grant no. 31003A_112670 and 310030_141067 to KJM and HFG). This project was further supported by the University of Zurich’s clinical research priority program: viral infectious diseases – ZPHI (to KJM and HFG). JI was supported by the Swiss National Science Foundation (in part) by a joint Sinergia grant (CRSII3_127454) to JH. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.