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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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Short-distance interactions supported both by consistency of prediction and covariation. Base pair covariations are indicated as boxes for qualifying base pairs. SHAPE values are indicated on a scale from black (low degree of flexibility) to red (high degree of flexibility). Missing SHAPE values at the start of the 5′ TAR hairpin are indicated in grey. The part of the RRE structure that did not pass the stringent filtering criteria is indicated in light blue. The structures that were not present in the most recent update of the Watts09 structure (22) are indicated with asterisk (*). Structure 9 is partially present in (22).
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Figure 6: Short-distance interactions supported both by consistency of prediction and covariation. Base pair covariations are indicated as boxes for qualifying base pairs. SHAPE values are indicated on a scale from black (low degree of flexibility) to red (high degree of flexibility). Missing SHAPE values at the start of the 5′ TAR hairpin are indicated in grey. The part of the RRE structure that did not pass the stringent filtering criteria is indicated in light blue. The structures that were not present in the most recent update of the Watts09 structure (22) are indicated with asterisk (*). Structure 9 is partially present in (22).

Mentions: Next, we identified the base pairs in the PPfold 3.1 prediction that were also present in at least 8 of the other 12 predictions. As expected, few structures were consistently predicted at this level of stringency: only 290 base pairs in 57 helices were present in at least 8 other predictions. To identify the structural elements that were also supported by base pair covariations, we further filtered the 57 helices according to the criteria described in the Materials and Methods section. After this filtering, 27 helices in 16 structural domains remained. The longest version of each helix was selected across all predictions, and these high-confidence substructures are depicted in Figure 6.


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)

Short-distance interactions supported both by consistency of prediction and covariation. Base pair covariations are indicated as boxes for qualifying base pairs. SHAPE values are indicated on a scale from black (low degree of flexibility) to red (high degree of flexibility). Missing SHAPE values at the start of the 5′ TAR hairpin are indicated in grey. The part of the RRE structure that did not pass the stringent filtering criteria is indicated in light blue. The structures that were not present in the most recent update of the Watts09 structure (22) are indicated with asterisk (*). Structure 9 is partially present in (22).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 6: Short-distance interactions supported both by consistency of prediction and covariation. Base pair covariations are indicated as boxes for qualifying base pairs. SHAPE values are indicated on a scale from black (low degree of flexibility) to red (high degree of flexibility). Missing SHAPE values at the start of the 5′ TAR hairpin are indicated in grey. The part of the RRE structure that did not pass the stringent filtering criteria is indicated in light blue. The structures that were not present in the most recent update of the Watts09 structure (22) are indicated with asterisk (*). Structure 9 is partially present in (22).
Mentions: Next, we identified the base pairs in the PPfold 3.1 prediction that were also present in at least 8 of the other 12 predictions. As expected, few structures were consistently predicted at this level of stringency: only 290 base pairs in 57 helices were present in at least 8 other predictions. To identify the structural elements that were also supported by base pair covariations, we further filtered the 57 helices according to the criteria described in the Materials and Methods section. After this filtering, 27 helices in 16 structural domains remained. The longest version of each helix was selected across all predictions, and these high-confidence substructures are depicted in Figure 6.

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