Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
Identifieur interne : 000B19 ( Main/Exploration ); précédent : 000B18; suivant : 000B20Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
Auteurs : Christine E. Hajdin ; Stanislav Bellaousov ; Wayne Huggins ; Christopher W. Leonard ; David H. Mathews ; Kevin M. WeeksSource :
- Proceedings of the National Academy of Sciences of the United States of America [ 0027-8424 ] ; 2013.
Abstract
A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified.
Url:
DOI: 10.1073/pnas.1219988110
PubMed: 23503844
PubMed Central: 3619282
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000474
- to stream Pmc, to step Curation: 000474
- to stream Pmc, to step Checkpoint: 000480
- to stream Ncbi, to step Merge: 000321
- to stream Ncbi, to step Curation: 000321
- to stream Ncbi, to step Checkpoint: 000321
- to stream Main, to step Merge: 000B21
- to stream Main, to step Curation: 000B19
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots</title><author><name sortKey="Hajdin, Christine E" sort="Hajdin, Christine E" uniqKey="Hajdin C" first="Christine E." last="Hajdin">Christine E. Hajdin</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author><author><name sortKey="Bellaousov, Stanislav" sort="Bellaousov, Stanislav" uniqKey="Bellaousov S" first="Stanislav" last="Bellaousov">Stanislav Bellaousov</name><affiliation><nlm:aff id="aff2">Department of Biochemistry and Biophysics, and Center for RNA Biology,<institution>University of Rochester Medical Center</institution>, Rochester,<addr-line>NY</addr-line> 14642</nlm:aff></affiliation></author><author><name sortKey="Huggins, Wayne" sort="Huggins, Wayne" uniqKey="Huggins W" first="Wayne" last="Huggins">Wayne Huggins</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author><author><name sortKey="Leonard, Christopher W" sort="Leonard, Christopher W" uniqKey="Leonard C" first="Christopher W." last="Leonard">Christopher W. Leonard</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author><author><name sortKey="Mathews, David H" sort="Mathews, David H" uniqKey="Mathews D" first="David H." last="Mathews">David H. Mathews</name><affiliation><nlm:aff id="aff2">Department of Biochemistry and Biophysics, and Center for RNA Biology,<institution>University of Rochester Medical Center</institution>, Rochester,<addr-line>NY</addr-line> 14642</nlm:aff></affiliation></author><author><name sortKey="Weeks, Kevin M" sort="Weeks, Kevin M" uniqKey="Weeks K" first="Kevin M." last="Weeks">Kevin M. Weeks</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23503844</idno><idno type="pmc">3619282</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619282</idno><idno type="RBID">PMC:3619282</idno><idno type="doi">10.1073/pnas.1219988110</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000474</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000474</idno><idno type="wicri:Area/Pmc/Curation">000474</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000474</idno><idno type="wicri:Area/Pmc/Checkpoint">000480</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000480</idno><idno type="wicri:Area/Ncbi/Merge">000321</idno><idno type="wicri:Area/Ncbi/Curation">000321</idno><idno type="wicri:Area/Ncbi/Checkpoint">000321</idno><idno type="wicri:doubleKey">0027-8424:2013:Hajdin C:accurate:shape:directed</idno><idno type="wicri:Area/Main/Merge">000B21</idno><idno type="wicri:Area/Main/Curation">000B19</idno><idno type="wicri:Area/Main/Exploration">000B19</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots</title><author><name sortKey="Hajdin, Christine E" sort="Hajdin, Christine E" uniqKey="Hajdin C" first="Christine E." last="Hajdin">Christine E. Hajdin</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author><author><name sortKey="Bellaousov, Stanislav" sort="Bellaousov, Stanislav" uniqKey="Bellaousov S" first="Stanislav" last="Bellaousov">Stanislav Bellaousov</name><affiliation><nlm:aff id="aff2">Department of Biochemistry and Biophysics, and Center for RNA Biology,<institution>University of Rochester Medical Center</institution>, Rochester,<addr-line>NY</addr-line> 14642</nlm:aff></affiliation></author><author><name sortKey="Huggins, Wayne" sort="Huggins, Wayne" uniqKey="Huggins W" first="Wayne" last="Huggins">Wayne Huggins</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author><author><name sortKey="Leonard, Christopher W" sort="Leonard, Christopher W" uniqKey="Leonard C" first="Christopher W." last="Leonard">Christopher W. Leonard</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author><author><name sortKey="Mathews, David H" sort="Mathews, David H" uniqKey="Mathews D" first="David H." last="Mathews">David H. Mathews</name><affiliation><nlm:aff id="aff2">Department of Biochemistry and Biophysics, and Center for RNA Biology,<institution>University of Rochester Medical Center</institution>, Rochester,<addr-line>NY</addr-line> 14642</nlm:aff></affiliation></author><author><name sortKey="Weeks, Kevin M" sort="Weeks, Kevin M" uniqKey="Weeks K" first="Kevin M." last="Weeks">Kevin M. Weeks</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="ISSN">0027-8424</idno><idno type="eISSN">1091-6490</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified.</p></div></front></TEI><affiliations><list></list><tree><noCountry><name sortKey="Bellaousov, Stanislav" sort="Bellaousov, Stanislav" uniqKey="Bellaousov S" first="Stanislav" last="Bellaousov">Stanislav Bellaousov</name><name sortKey="Hajdin, Christine E" sort="Hajdin, Christine E" uniqKey="Hajdin C" first="Christine E." last="Hajdin">Christine E. Hajdin</name><name sortKey="Huggins, Wayne" sort="Huggins, Wayne" uniqKey="Huggins W" first="Wayne" last="Huggins">Wayne Huggins</name><name sortKey="Leonard, Christopher W" sort="Leonard, Christopher W" uniqKey="Leonard C" first="Christopher W." last="Leonard">Christopher W. Leonard</name><name sortKey="Mathews, David H" sort="Mathews, David H" uniqKey="Mathews D" first="David H." last="Mathews">David H. Mathews</name><name sortKey="Weeks, Kevin M" sort="Weeks, Kevin M" uniqKey="Weeks K" first="Kevin M." last="Weeks">Kevin M. Weeks</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/CovidV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000B19 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000B19 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Sante
|area= CovidV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:3619282
|texte= Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:23503844" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a CovidV1
| This area was generated with Dilib version V0.6.33. |  |