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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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A comparative model for the secondary structure of the HIV-1 genome, predicted with PPfold 3.1, integrating covariation information from a manually curated alignment of 38 HIV-1 genome sequences and structure probing data from the SHAPE method. Each nucleotide is coloured according to the reliability score (described in Materials and Methods). Long-distance interactions (further than 600 nucleotides apart) are indicated with letter codes. Corresponding capital and non-capital letters interact. A higher resolution version of the figure with nucleotide identities is available in Supplementary Figure S2.
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Figure 1: A comparative model for the secondary structure of the HIV-1 genome, predicted with PPfold 3.1, integrating covariation information from a manually curated alignment of 38 HIV-1 genome sequences and structure probing data from the SHAPE method. Each nucleotide is coloured according to the reliability score (described in Materials and Methods). Long-distance interactions (further than 600 nucleotides apart) are indicated with letter codes. Corresponding capital and non-capital letters interact. A higher resolution version of the figure with nucleotide identities is available in Supplementary Figure S2.

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.


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)

A comparative model for the secondary structure of the HIV-1 genome, predicted with PPfold 3.1, integrating covariation information from a manually curated alignment of 38 HIV-1 genome sequences and structure probing data from the SHAPE method. Each nucleotide is coloured according to the reliability score (described in Materials and Methods). Long-distance interactions (further than 600 nucleotides apart) are indicated with letter codes. Corresponding capital and non-capital letters interact. A higher resolution version of the figure with nucleotide identities is available in Supplementary Figure S2.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: A comparative model for the secondary structure of the HIV-1 genome, predicted with PPfold 3.1, integrating covariation information from a manually curated alignment of 38 HIV-1 genome sequences and structure probing data from the SHAPE method. Each nucleotide is coloured according to the reliability score (described in Materials and Methods). Long-distance interactions (further than 600 nucleotides apart) are indicated with letter codes. Corresponding capital and non-capital letters interact. A higher resolution version of the figure with nucleotide identities is available in Supplementary Figure S2.
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.

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