title: U3 region in the HIV-1 genome adopts a G-quadruplex structure in its RNA and DNA sequence.
abstract: Genomic regions rich in G residues are prone to adopt G-quadruplex structure. Multiple Sp1-binding motifs arranged in tandem have been suggested to form this structure in promoters of cancer-related genes. Here, we demonstrate that the G-rich proviral DNA sequence of the HIV-1 U3 region, which serves as a promoter of viral transcription, adopts a G-quadruplex structure. The sequence contains three binding elements for transcription factor Sp1, which is involved in the regulation of HIV-1 latency, reactivation, and high-level virus expression. We show that the three Sp1 binding motifs can adopt different forms of G-quadruplex structure and that the Sp1 protein can recognize and bind to its site folded into a G-quadruplex. In addition, a c-kit2 specific antibody, designated hf2, binds to two different G-quadruplexes formed in Sp1 sites. Since U3 is encoded at both viral genomic ends, the G-rich sequence is also present in the RNA genome. We demonstrate that the RNA sequence of U3 forms dimers with characteristics known for intermolecular G-quadruplexes. Together with previous reports showing G-quadruplex dimers in the gag and cPPT regions, these results suggest that integrity of the two viral genomes is maintained through numerous intermolecular G-quadruplexes formed in different RNA genome locations. Reconstituted reverse transcription shows that the potassium-dependent structure formed in U3 RNA facilitates RT template switching, suggesting that the G-quadruplex contributes to recombination in U3.
authors.affiliation: Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester , Rochester, New York 14642, United States.
authors.forename: Dorota
authors.initials: D
authors.lastname: Piekna-Przybylska
authors.forename: Mark A
authors.initials: MA
authors.lastname: Sullivan
authors.forename: Gaurav
authors.initials: G
authors.lastname: Sharma
authors.forename: Robert A
authors.initials: RA
authors.lastname: Bambara
mesh_terms: D001665:Binding Sites; D002942:Circular Dichroism; D004277:DNA, Single-Stranded / Q000737:chemistry; D004279:DNA, Viral / Q000737:chemistry; D019281:Dimerization; D054856:G-Quadruplexes; D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics*; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D020537:RNA, Small Nucleolar / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry; D016329:Sp1 Transcription Factor / Q000378:metabolism
chemical_list: D004277:DNA, Single-Stranded; D004279:DNA, Viral; D020537:RNA, Small Nucleolar; C117378:RNA, U3 small nucleolar; D012367:RNA, Viral; D016329:Sp1 Transcription Factor
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