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

Sükösd Z, Andersen ES, Seemann SE, Jensen MK, Hansen M, Gorodkin J, Kjems J - Nucleic Acids Res. (2015)

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.

View Article: PubMed Central - PubMed

Affiliation: BiRC, Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark zsuzsanna.etches@qiagen.com.

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Related in: MedlinePlus

The PPfold 3.1 structure coloured by comparison with the Watts09 structure. The predictions were made with identical SHAPE data. Common structural elements are indicated in red (base pairs) and blue (unpaired nucleotides). Elements paired in both structures (but with different partners) are indicated by yellow. Nucleotides paired in one but unpaired in the other are indicated in brown. 72% of all unpaired nucleotides and 31% of base paired nucleotides were found in both predictions. Over half of the genome is unpaired in both predictions (blue). A higher resolution version of the figure with nucleotide identities is available in Supplementary Figure S3.
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Figure 3: The PPfold 3.1 structure coloured by comparison with the Watts09 structure. The predictions were made with identical SHAPE data. Common structural elements are indicated in red (base pairs) and blue (unpaired nucleotides). Elements paired in both structures (but with different partners) are indicated by yellow. Nucleotides paired in one but unpaired in the other are indicated in brown. 72% of all unpaired nucleotides and 31% of base paired nucleotides were found in both predictions. Over half of the genome is unpaired in both predictions (blue). A higher resolution version of the figure with nucleotide identities is available in Supplementary Figure S3.

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.


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

Sükösd Z, Andersen ES, Seemann SE, Jensen MK, Hansen M, Gorodkin J, Kjems J - Nucleic Acids Res. (2015)

The PPfold 3.1 structure coloured by comparison with the Watts09 structure. The predictions were made with identical SHAPE data. Common structural elements are indicated in red (base pairs) and blue (unpaired nucleotides). Elements paired in both structures (but with different partners) are indicated by yellow. Nucleotides paired in one but unpaired in the other are indicated in brown. 72% of all unpaired nucleotides and 31% of base paired nucleotides were found in both predictions. Over half of the genome is unpaired in both predictions (blue). A higher resolution version of the figure with nucleotide identities is available in Supplementary Figure S3.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4666355&req=5

Figure 3: The PPfold 3.1 structure coloured by comparison with the Watts09 structure. The predictions were made with identical SHAPE data. Common structural elements are indicated in red (base pairs) and blue (unpaired nucleotides). Elements paired in both structures (but with different partners) are indicated by yellow. Nucleotides paired in one but unpaired in the other are indicated in brown. 72% of all unpaired nucleotides and 31% of base paired nucleotides were found in both predictions. Over half of the genome is unpaired in both predictions (blue). A higher resolution version of the figure with nucleotide identities is available in Supplementary Figure S3.
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.

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.

View Article: PubMed Central - PubMed

Affiliation: BiRC, Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark zsuzsanna.etches@qiagen.com.

Show MeSH
Related in: MedlinePlus