title: HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: University Hospital Zurich, Division of Infectious Diseases and Hospital Epidemiology, University of Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
authors.forename: Valentina
authors.initials: V
authors.lastname: Vongrad
authors.affiliation: ETH Zurich, Institute of Pharmaceutical Sciences, Zurich, Switzerland.
authors.forename: Jochen
authors.initials: J
authors.lastname: Imig
authors.affiliation: ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
authors.forename: Pejman
authors.initials: P
authors.lastname: Mohammadi
authors.affiliation: University of Basel, Computational and Systems Biology, Basel, Switzerland.
authors.forename: Shivendra
authors.initials: S
authors.lastname: Kishore
authors.affiliation: University of Basel, Computational and Systems Biology, Basel, Switzerland.
authors.forename: Lukasz
authors.initials: L
authors.lastname: Jaskiewicz
authors.affiliation: ETH Zurich, Institute of Pharmaceutical Sciences, Zurich, Switzerland.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Hall
authors.affiliation: University Hospital Zurich, Division of Infectious Diseases and Hospital Epidemiology, University of Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
authors.forename: Huldrych F
authors.initials: HF
authors.lastname: Günthard
authors.affiliation: ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
authors.forename: Niko
authors.initials: N
authors.lastname: Beerenwinkel
authors.affiliation: University Hospital Zurich, Division of Infectious Diseases and Hospital Epidemiology, University of Zurich, Zurich, Switzerland; Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
authors.forename: Karin J
authors.initials: KJ
authors.lastname: Metzner
mesh_terms: D060565:Argonaute Proteins / Q000235:genetics*; D001483:Base Sequence; D002460:Cell Line; D005786:Gene Expression Regulation; D057809:HEK293 Cells; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008264:Macrophages / Q000276:immunology*; D035683:MicroRNAs / Q000235:genetics; D034622:RNA Interference; D012367:RNA, Viral / Q000235:genetics*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
chemical_list: C466422:AGO2 protein, human; D060565:Argonaute Proteins; D035683:MicroRNAs; D012367:RNA, Viral