title: Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats.
abstract: BACKGROUND
  HIV infection has been reported to alter cellular gene activity, but published studies have commonly assayed transformed cell lines and lab-adapted HIV strains, yielding inconsistent results. Here we carried out a deep RNA-Seq analysis of primary human T cells infected with the low passage HIV isolate HIV89.6.
  
  
  RESULTS
  Seventeen percent of cellular genes showed altered activity 48 h after infection. In a meta-analysis including four other studies, our data differed from studies of HIV infection in cell lines but showed more parallels with infections of primary cells. We found a global trend toward retention of introns after infection, suggestive of a novel cellular response to infection. HIV89.6 infection was also associated with activation of several human endogenous retroviruses (HERVs) and retrotransposons, of interest as possible novel antigens that could serve as vaccine targets. The most highly activated group of HERVs was a subset of the ERV-9. Analysis showed that activation was associated with a particular variant of ERV-9 long terminal repeats that contains an indel near the U3-R border. These data also allowed quantification of >70 splice forms of the HIV89.6 RNA and specified the main types of chimeric HIV89.6-host RNAs. Comparison to over 100,000 integration site sequences from the same infected cell populations allowed quantification of authentic versus artifactual chimeric reads, showing that 5' read-in, splicing out of HIV89.6 from the D4 donor and 3' read-through were the most common HIV89.6-host cell chimeric RNA forms.
  
  
  CONCLUSIONS
  Analysis of RNA abundance after infection of primary T cells with the low passage HIV89.6 isolate disclosed multiple novel features of HIV-host interactions, notably intron retention and induction of transcription of retrotransposons and endogenous retroviruses.
authors.affiliation: Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA. shescott@mail.med.upenn.edu.
authors.forename: Scott
authors.initials: S
authors.lastname: Sherrill-Mix
authors.affiliation: Children's Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA, 19104, USA. ocwiejak@email.chop.edu.
authors.forename: Karen E
authors.initials: KE
authors.lastname: Ocwieja
authors.affiliation: Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA. bushman@mail.med.upenn.edu.
authors.forename: Frederic D
authors.initials: FD
authors.lastname: Bushman
mesh_terms: D002460:Cell Line; D002478:Cells, Cultured; D020077:Endogenous Retroviruses / Q000502:physiology; D015497:HIV-1 / Q000502:physiology*; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions; D006801:Humans; D007438:Introns; D018626:Retroelements; D013601:T-Lymphocytes / Q000378:metabolism* / Q000821:virology*; D015533:Transcriptional Activation; D014775:Virus Activation
chemical_list: D018626:Retroelements