title: Identification of unusual and novel HIV type 1 spliced transcripts generated in vivo.
abstract: HIV-1 transcripts are generated through a complex alternative splicing mechanism, resulting in the production of multiple RNAs coding for each viral protein. HIV-1 RNA splicing has been analyzed mostly in in vitro assays, and in vivo data are scarce. Here we analyze HIV-1 transcripts generated in peripheral blood mononuclear cells of HIV-1-infected individuals by RT-PCR amplification and sequencing of RNA extracted from unstimulated cells. We identify several unusual or unreported transcripts, most of them splicing within the Nef coding sequence. The majority are predicted to code for a Nef C-terminal 34 amino acid peptide, but others code for Vpr, a truncated Tat, and a 41 amino acid peptide encoded in an antisense exon. We also identify nef and env transcripts splicing four nucleotides downstream of SA5. These results represent the first report on the in vivo generation of diverse novel HIV-1-spliced transcripts, frequently encoding a Nef C-terminal peptide.
authors.affiliation: Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: Carrera
authors.forename: Milagros
authors.initials: M
authors.lastname: Pinilla
authors.forename: Lucía
authors.initials: L
authors.lastname: Pérez-Alvarez
authors.forename: Michael M
authors.initials: MM
authors.lastname: Thomson
mesh_terms: D002478:Cells, Cultured; D015870:Gene Expression; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000502:physiology*; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000821:virology; D008969:Molecular Sequence Data; D020033:Protein Isoforms / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics; D054311:nef Gene Products, Human Immunodeficiency Virus / Q000235:genetics; D054322:tat Gene Products, Human Immunodeficiency Virus / Q000235:genetics; D054325:vpr Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D020033:Protein Isoforms; D012367:RNA, Viral; D054299:env Gene Products, Human Immunodeficiency Virus; D054311:nef Gene Products, Human Immunodeficiency Virus; C514837:nef protein, Human immunodeficiency virus 1; D054322:tat Gene Products, Human Immunodeficiency Virus; D054325:vpr Gene Products, Human Immunodeficiency Virus; C514912:vpr protein, Human immunodeficiency virus 1