title: Analysis of HIV-1 expression level and sense of transcription by high-throughput sequencing of the infected cell.
abstract: Next-generation sequencing offers an unprecedented opportunity to jointly analyze cellular and viral transcriptional activity without prerequisite knowledge of the nature of the transcripts. SupT1 cells were infected with a vesicular stomatitis virus G envelope protein (VSV-G)-pseudotyped HIV vector. At 24 h postinfection, both cellular and viral transcriptomes were analyzed by serial analysis of gene expression followed by high-throughput sequencing (SAGE-Seq). Read mapping resulted in 33 to 44 million tags aligning with the human transcriptome and 0.23 to 0.25 million tags aligning with the genome of the HIV-1 vector. Thus, at peak infection, 1 transcript in 143 is of viral origin (0.7%), including a small component of antisense viral transcription. Of the detected cellular transcripts, 826 (2.3%) were differentially expressed between mock- and HIV-infected samples. The approach also assessed whether HIV-1 infection modulates the expression of repetitive elements or endogenous retroviruses. We observed very active transcription of these elements, with 1 transcript in 237 being of such origin, corresponding on average to 123,123 reads in mock-infected samples (0.40%) and 129,149 reads in HIV-1-infected samples (0.45%) mapping to the genomic Repbase repository. This analysis highlights key details in the generation and interpretation of high-throughput data in the setting of HIV-1 cellular infection.
authors.affiliation: Institute of Microbiology, University Hospital Center and University of Lausanne, Bugnon 48, CH-1011 Lausanne, Switzerland.
authors.forename: Gregory
authors.initials: G
authors.lastname: Lefebvre
authors.forename: Sébastien
authors.initials: S
authors.lastname: Desfarges
authors.forename: Frédéric
authors.initials: F
authors.lastname: Uyttebroeck
authors.forename: Miguel
authors.initials: M
authors.lastname: Muñoz
authors.forename: Niko
authors.initials: N
authors.lastname: Beerenwinkel
authors.forename: Jacques
authors.initials: J
authors.lastname: Rougemont
authors.forename: Amalio
authors.initials: A
authors.lastname: Telenti
authors.forename: Angela
authors.initials: A
authors.lastname: Ciuffi
mesh_terms: D002460:Cell Line; D020869:Gene Expression Profiling; D005822:Genetic Vectors / Q000235:genetics; D015658:HIV Infections / Q000821:virology; D015497:HIV-1 / Q000235:genetics / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008562:Membrane Glycoproteins / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism; D016324:Sequence Tagged Sites; D013601:T-Lymphocytes / Q000378:metabolism* / Q000821:virology*; D014158:Transcription, Genetic; D014759:Viral Envelope Proteins / Q000235:genetics / Q000378:metabolism; D014779:Virus Replication
chemical_list: C028391:G protein, vesicular stomatitis virus; D008562:Membrane Glycoproteins; D012333:RNA, Messenger; D012367:RNA, Viral; D014759:Viral Envelope Proteins