Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
Identifieur interne : 000480 ( Pmc/Checkpoint ); précédent : 000479; suivant : 000481Accurate 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:
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<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>
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<front><journal-meta><journal-id journal-id-type="nlm-ta">Proc Natl Acad Sci U S A</journal-id>
<journal-id journal-id-type="iso-abbrev">Proc. Natl. Acad. Sci. U.S.A</journal-id>
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<article-id pub-id-type="doi">10.1073/pnas.1219988110</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Biological Sciences</subject>
<subj-group><subject>Biophysics and Computational Biology</subject>
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<title-group><article-title>Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots</article-title>
<alt-title alt-title-type="short">SHAPE-directed RNA structure modeling</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Hajdin</surname>
<given-names>Christine E.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
<xref ref-type="author-notes" rid="fn1"><sup>1</sup>
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<contrib contrib-type="author"><name><surname>Bellaousov</surname>
<given-names>Stanislav</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
<xref ref-type="author-notes" rid="fn1"><sup>1</sup>
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<contrib contrib-type="author"><name><surname>Huggins</surname>
<given-names>Wayne</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Leonard</surname>
<given-names>Christopher W.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
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<contrib contrib-type="author"><name><surname>Mathews</surname>
<given-names>David H.</given-names>
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<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>2</sup>
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<contrib contrib-type="author"><name><surname>Weeks</surname>
<given-names>Kevin M.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>2</sup>
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<aff id="aff1"><sup>a</sup>
Department of Chemistry,<institution>University of North Carolina</institution>
, Chapel Hill,<addr-line>NC</addr-line>
27599-3290; and</aff>
<aff id="aff2"><sup>b</sup>
Department of Biochemistry and Biophysics, and Center for RNA Biology,<institution>University of Rochester Medical Center</institution>
, Rochester,<addr-line>NY</addr-line>
14642</aff>
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<author-notes><corresp id="cor1"><sup>2</sup>
To whom correspondence may be addressed. E-mail: <email>weeks@unc.edu</email>
or <email>David_Mathews@urmc.rochester.edu</email>
.</corresp>
<fn fn-type="edited-by"><p>Edited by Ignacio Tinoco, University of California, Berkeley, CA, and approved February 5, 2013 (received for review November 15, 2012)</p>
</fn>
<fn fn-type="con"><p>Author contributions: C.E.H., S.B., W.H., D.H.M., and K.M.W. designed research; C.E.H., S.B., W.H., and C.W.L. performed research; C.E.H., S.B., W.H., C.W.L., D.H.M., and K.M.W. analyzed data; and C.E.H., S.B., D.H.M., and K.M.W. wrote the paper.</p>
</fn>
<fn id="fn1" fn-type="equal"><p><sup>1</sup>
C.E.H. and S.B. contributed equally to this work.</p>
</fn>
<fn fn-type="conflict"><p>The authors declare no conflict of interest.</p>
</fn>
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<abstract><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>
</abstract>
<kwd-group><kwd>thermodynamics</kwd>
<kwd>nearest neighbor parameters</kwd>
<kwd>circle plot</kwd>
<kwd>polymer model</kwd>
<kwd>1M7</kwd>
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<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>
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