Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain.
Bottom Line: 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.
Affiliation: BiRC, Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark firstname.lastname@example.org.Show MeSH
Related in: MedlinePlus
Mentions: We predicted the consensus secondary structure of an HIV-1 alignment using PPfold 3.1, which is a re-implementation of the Pfold algorithm (38) extended with probabilistic support for RNA probing data (23). As input, we used a manually curated alignment of sequences from HIV-1 subtypes A-K (excluding strain G; see Materials and Methods), and the experimental SHAPE data from (7). In order to maximize useful phylogenetic information and minimize noise (39), we predicted the HIV-1 structure from 38 representative sequences, as described in Materials and Methods (Figures 1 and 2). A larger alignment of 1851 HIV-1 sequences was then used as an independent evaluation of the phylogenetic evidence for the predicted structures.
Affiliation: BiRC, Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark email@example.com.