title: Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain.
abstract: A distance constrained secondary structural model of the ≈10 kb RNA genome of the HIV-1 has been predicted but higher-order structures, involving long distance interactions, are currently unknown. We present the first global RNA secondary structure model for the HIV-1 genome, which integrates both comparative structure analysis and information from experimental data in a full-length prediction without distance constraints. Besides recovering known structural elements, we predict several novel structural elements that are conserved in HIV-1 evolution. Our results also indicate that the structure of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping protein-coding regions the COS is supported by a particular high frequency of compensatory base changes, suggesting functional importance for this element. This new structural element potentially organizes the whole genome into three major domains protruding from a conserved core structure with potential roles in replication and evolution for the virus.
authors.affiliation: BiRC, Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark zsuzsanna.etches@qiagen.com.
authors.forename: Zsuzsanna
authors.initials: Z
authors.lastname: Sükösd
authors.affiliation: iNANO, Interdisciplinary Nanoscience Center, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Ebbe S
authors.initials: ES
authors.lastname: Andersen
authors.affiliation: RTH, Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark.
authors.forename: Stefan E
authors.initials: SE
authors.lastname: Seemann
authors.affiliation: BiRC, Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Mads Krogh
authors.initials: MK
authors.lastname: Jensen
authors.affiliation: BiRC, Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Mathias
authors.initials: M
authors.lastname: Hansen
authors.affiliation: RTH, Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark.
authors.forename: Jan
authors.initials: J
authors.lastname: Gorodkin
authors.affiliation: iNANO, Interdisciplinary Nanoscience Center, Aarhus University, DK-8000 Aarhus C, Denmark jk@mb.au.dk.
authors.forename: Jørgen
authors.initials: J
authors.lastname: Kjems
mesh_terms: D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics*; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry*; D012984:Software
chemical_list: D012367:RNA, Viral