Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain

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DOI

  • Zsuzsanna Sukosd
  • ,
  • Ebbe S. Andersen
  • Stefan E. Seemann, Univ Copenhagen, University of Copenhagen, RTH, Ctr Noncoding RNA Technol & Hlth, Dept Vet Clin & Anim Sci
  • ,
  • Mads Jensen, Denmark
  • Mathias Brygger Hansen, Denmark
  • Jan Gorodkin, Univ Copenhagen, University of Copenhagen, RTH, Ctr Noncoding RNA Technol & Hlth, Dept Vet Clin & Anim Sci
  • ,
  • Jørgen Kjems

A distance constrained secondary structural model of the approximate to 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.

Original languageEnglish
JournalNucleic Acids Research
Volume43
Issue21
Pages (from-to)10168-10179
Number of pages12
ISSN0305-1048
DOIs
Publication statusPublished - 2 Dec 2015

    Research areas

  • SECONDARY STRUCTURE PREDICTION, IMMUNODEFICIENCY-VIRUS TYPE-1, CONSENSUS STRUCTURE PREDICTION, CONTEXT-FREE GRAMMARS, EVOLUTIONARY, DIMERIZATION, REGION, SHAPE, GENE, CIRCULARIZATION

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