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: The structures predicted by PPfold 3.1 and Watts09 were compared and similarities and differences are colour coded in Figure 3. It is clear that several short-distance structural elements are shared between the Watts09 model and our prediction (red helices and blue single stranded regions). However, it is also immediately apparent that our structure is significantly different from the Watts09 structure, with only 31% of the base pairs (92 helices) in common. As both predictions are based in part on the same SHAPE data, an assessment of the differences requires additional analysis.
Affiliation: BiRC, Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark email@example.com.