title: Long sequence duplications, repeats, and palindromes in HIV-1 gp120: length variation in V4 as the product of misalignment mechanism.
abstract: We have shown that indels in gp120 V4 are associated to the presence of duplicated and palindromic sequences, suggesting that they may be produced by strand-slippage misalignment mechanism. Indels in V4 involved region-specific duplications 9 to 15 bp long, and repeats of various lengths, associated to trinucleotides AAT. No duplications were found in V3 and C3. The frequency of palindromic sequences in individual genes was found to be significantly higher in gp120 (p < or = 3.00E-7), and significantly lower in Tat (p < or = 9.00E-7) than the average frequency calculated over the full genome. The finding of elements of misalignment in association with indels in V4 suggests that these mutations may occur in proviral DNA after integration of HIV into the host genome. It also implies that occurrence of large indels in gp120 is not random but is directed by the presence and distribution of elements of misalignment in the HIV genome.
authors.affiliation: Laboratory of AIDS Immunopathogenesis, Division of Immunology and Allergy, Department of Medicine, CHUV, Hôpital Beaumont, 29, Ave Beaumont, Rm. 02-36 CHUV, 1011 Lausanne, Switzerland. Electronic address: Silvia.Guglietta@chuv.ch.
authors.forename: Silvia
authors.initials: S
authors.lastname: Guglietta
authors.affiliation: Laboratory of AIDS Immunopathogenesis, Division of Immunology and Allergy, Department of Medicine, CHUV, Hôpital Beaumont, 29, Ave Beaumont, Rm. 02-36 CHUV, 1011 Lausanne, Switzerland; Division of Immunology and Allergy, Department of Medicine, CHUV 46, Rue du Bugnon 1011 Lausanne, Switzerland. Electronic address: Giuseppe.Pantaleo@chuv.ch.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Pantaleo
authors.affiliation: Laboratory of AIDS Immunopathogenesis, Division of Immunology and Allergy, Department of Medicine, CHUV, Hôpital Beaumont, 29, Ave Beaumont, Rm. 02-36 CHUV, 1011 Lausanne, Switzerland. Electronic address: cecilia.graziosi@chuv.ch.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Graziosi
mesh_terms: D001483:Base Sequence; D016368:Frameshift Mutation / Q000235:genetics; D015752:Genes, env / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D015699:HIV Envelope Protein gp120 / Q000235:genetics*; D015658:HIV Infections / Q000821:virology; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D055029:Inverted Repeat Sequences / Q000235:genetics*; D016254:Mutagenesis, Insertional / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D018911:Trinucleotide Repeats / Q000235:genetics
chemical_list: D015699:HIV Envelope Protein gp120; C514793:gp120 protein, Human immunodeficiency virus 1