Structural basis for triplet repeat disorders: a computational analysis.
Identifieur interne : 002597 ( PubMed/Curation ); précédent : 002596; suivant : 002598Structural basis for triplet repeat disorders: a computational analysis.
Auteurs : P. Baldi [États-Unis] ; S. Brunak ; Y. Chauvin ; A G PedersenSource :
- Bioinformatics (Oxford, England) [ 1367-4803 ] ; 1999.
Descripteurs français
- KwdFr :
- ADN (), ADN (génétique), ADN (métabolisme), Anticipation génétique, Atrophie multisystématisée (génétique), Conformation d'acide nucléique, Deoxyribonuclease I (métabolisme), Expansion de trinucléotide répété (génétique), Flexibilité, Humains, Liaison aux protéines (génétique), Maladies génétiques congénitales (génétique), Modèles génétiques, Nucléosomes (génétique), Nucléosomes (métabolisme), Protéines de tissu nerveux (génétique), Protéines de transport (génétique), Répétitions de trinucléotides (génétique), Simulation numérique.
- MESH :
- génétique : ADN, Atrophie multisystématisée, Expansion de trinucléotide répété, Liaison aux protéines, Maladies génétiques congénitales, Nucléosomes, Protéines de tissu nerveux, Protéines de transport, Répétitions de trinucléotides.
- métabolisme : ADN, Deoxyribonuclease I, Nucléosomes.
- ADN, Anticipation génétique, Conformation d'acide nucléique, Flexibilité, Humains, Modèles génétiques, Simulation numérique.
English descriptors
- KwdEn :
- Anticipation, Genetic, Carrier Proteins (genetics), Computer Simulation, DNA (chemistry), DNA (genetics), DNA (metabolism), Deoxyribonuclease I (metabolism), Genetic Diseases, Inborn (genetics), Humans, Models, Genetic, Multiple System Atrophy (genetics), Nerve Tissue Proteins (genetics), Nucleic Acid Conformation, Nucleosomes (genetics), Nucleosomes (metabolism), Pliability, Protein Binding (genetics), Trinucleotide Repeat Expansion (genetics), Trinucleotide Repeats (genetics).
- MESH :
- chemical , chemistry : DNA.
- chemical , genetics : Carrier Proteins, DNA, Nerve Tissue Proteins, Nucleosomes.
- chemical , metabolism : DNA, Deoxyribonuclease I, Nucleosomes.
- genetics : Genetic Diseases, Inborn, Multiple System Atrophy, Protein Binding, Trinucleotide Repeat Expansion, Trinucleotide Repeats.
- Anticipation, Genetic, Computer Simulation, Humans, Models, Genetic, Nucleic Acid Conformation, Pliability.
Abstract
Over a dozen major degenerative disorders, including myotonic distrophy, Huntington's disease and fragile X syndrome, result from unstable expansions of particular trinucleotides. Remarkably, only some of all the possible triplets, namely CAG/CTG, CGG/CCG and GAA/TTC, have been associated with the known pathological expansions. This raises some basic questions at the DNA level. Why do particular triplets seem to be singled out? What is the mechanism for their expansion and how does it depend on the triplet itself? Could other triplets or longer repeats be involved in other diseases?
DOI: 10.1093/bioinformatics/15.11.918
PubMed: 10743558
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Chauvin</name></author><author><name sortKey="Pedersen, A G" sort="Pedersen, A G" uniqKey="Pedersen A" first="A G" last="Pedersen">A G Pedersen</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="1999">1999</date><idno type="RBID">pubmed:10743558</idno><idno type="pmid">10743558</idno><idno type="doi">10.1093/bioinformatics/15.11.918</idno><idno type="wicri:Area/PubMed/Corpus">002597</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002597</idno><idno type="wicri:Area/PubMed/Curation">002597</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002597</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Structural basis for triplet repeat disorders: a computational analysis.</title><author><name sortKey="Baldi, P" sort="Baldi, P" uniqKey="Baldi P" first="P" last="Baldi">P. Baldi</name><affiliation wicri:level="1"><nlm:affiliation>Department of Information and Computer Science, College of Medicine, University of California, Irvine 92697-3425, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Information and Computer Science, College of Medicine, University of California, Irvine 92697-3425</wicri:regionArea></affiliation></author><author><name sortKey="Brunak, S" sort="Brunak, S" uniqKey="Brunak S" first="S" last="Brunak">S. Brunak</name></author><author><name sortKey="Chauvin, Y" sort="Chauvin, Y" uniqKey="Chauvin Y" first="Y" last="Chauvin">Y. Chauvin</name></author><author><name sortKey="Pedersen, A G" sort="Pedersen, A G" uniqKey="Pedersen A" first="A G" last="Pedersen">A G Pedersen</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="ISSN">1367-4803</idno><imprint><date when="1999" type="published">1999</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Anticipation, Genetic</term><term>Carrier Proteins (genetics)</term><term>Computer Simulation</term><term>DNA (chemistry)</term><term>DNA (genetics)</term><term>DNA (metabolism)</term><term>Deoxyribonuclease I (metabolism)</term><term>Genetic Diseases, Inborn (genetics)</term><term>Humans</term><term>Models, Genetic</term><term>Multiple System Atrophy (genetics)</term><term>Nerve Tissue Proteins (genetics)</term><term>Nucleic Acid Conformation</term><term>Nucleosomes (genetics)</term><term>Nucleosomes (metabolism)</term><term>Pliability</term><term>Protein Binding (genetics)</term><term>Trinucleotide Repeat Expansion (genetics)</term><term>Trinucleotide Repeats (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>ADN (génétique)</term><term>ADN (métabolisme)</term><term>Anticipation génétique</term><term>Atrophie multisystématisée (génétique)</term><term>Conformation d'acide nucléique</term><term>Deoxyribonuclease I (métabolisme)</term><term>Expansion de trinucléotide répété (génétique)</term><term>Flexibilité</term><term>Humains</term><term>Liaison aux protéines (génétique)</term><term>Maladies génétiques congénitales (génétique)</term><term>Modèles génétiques</term><term>Nucléosomes (génétique)</term><term>Nucléosomes (métabolisme)</term><term>Protéines de tissu nerveux (génétique)</term><term>Protéines de transport (génétique)</term><term>Répétitions de trinucléotides (génétique)</term><term>Simulation numérique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Carrier Proteins</term><term>DNA</term><term>Nerve Tissue Proteins</term><term>Nucleosomes</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA</term><term>Deoxyribonuclease I</term><term>Nucleosomes</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genetic Diseases, Inborn</term><term>Multiple System Atrophy</term><term>Protein Binding</term><term>Trinucleotide Repeat Expansion</term><term>Trinucleotide Repeats</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN</term><term>Atrophie multisystématisée</term><term>Expansion de trinucléotide répété</term><term>Liaison aux protéines</term><term>Maladies génétiques congénitales</term><term>Nucléosomes</term><term>Protéines de tissu nerveux</term><term>Protéines de transport</term><term>Répétitions de trinucléotides</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN</term><term>Deoxyribonuclease I</term><term>Nucléosomes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Anticipation, Genetic</term><term>Computer Simulation</term><term>Humans</term><term>Models, Genetic</term><term>Nucleic Acid Conformation</term><term>Pliability</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Anticipation génétique</term><term>Conformation d'acide nucléique</term><term>Flexibilité</term><term>Humains</term><term>Modèles génétiques</term><term>Simulation numérique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Over a dozen major degenerative disorders, including myotonic distrophy, Huntington's disease and fragile X syndrome, result from unstable expansions of particular trinucleotides. Remarkably, only some of all the possible triplets, namely CAG/CTG, CGG/CCG and GAA/TTC, have been associated with the known pathological expansions. This raises some basic questions at the DNA level. Why do particular triplets seem to be singled out? What is the mechanism for their expansion and how does it depend on the triplet itself? Could other triplets or longer repeats be involved in other diseases?</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">10743558</PMID><DateCompleted><Year>2000</Year><Month>05</Month><Day>25</Day></DateCompleted><DateRevised><Year>2019</Year><Month>05</Month><Day>13</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">1367-4803</ISSN><JournalIssue CitedMedium="Print"><Volume>15</Volume><Issue>11</Issue><PubDate><Year>1999</Year><Month>Nov</Month></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Structural basis for triplet repeat disorders: a computational analysis.</ArticleTitle><Pagination><MedlinePgn>918-29</MedlinePgn></Pagination><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">Over a dozen major degenerative disorders, including myotonic distrophy, Huntington's disease and fragile X syndrome, result from unstable expansions of particular trinucleotides. Remarkably, only some of all the possible triplets, namely CAG/CTG, CGG/CCG and GAA/TTC, have been associated with the known pathological expansions. This raises some basic questions at the DNA level. Why do particular triplets seem to be singled out? What is the mechanism for their expansion and how does it depend on the triplet itself? Could other triplets or longer repeats be involved in other diseases?</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Using several different computational models of DNA structure, we show that the triplets involved in the pathological repeats generally fall into extreme classes. Thus, CAG/CTG repeats are particularly flexible, whereas GCC, CGG and GAA repeats appear to display both flexible and rigid (but curved) characteristics depending on the method of analysis. The fact that (1) trinucleotide repeats often become increasingly unstable when they exceed a length of approximately 50 repeats, and (2) repeated 12-mers display a similar increase in instability above 13 repeats, together suggest that approximately 150 bp is a general threshold length for repeat instability. Since this is about the length of DNA wrapped up in a single nucleosome core particle, we speculate that chromatin structure may play an important role in the expansion mechanism. We furthermore suggest that expansion of a dodecamer repeat, which we predict to have very high flexibility, may play a role in the pathogenesis of the neurodegenerative disorder multiple system atrophy (MSA).</AbstractText><AbstractText Label="CONTACT" NlmCategory="BACKGROUND">pfbaldi@ics.uci.edu, yves@netid.com, brunak@cbs.dtu.dk, gorm@cbs.dtu.dk.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Baldi</LastName><ForeName>P</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Information and Computer Science, College of Medicine, University of California, Irvine 92697-3425, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Brunak</LastName><ForeName>S</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Chauvin</LastName><ForeName>Y</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Pedersen</LastName><ForeName>A G</ForeName><Initials>AG</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013487">Research Support, U.S. Gov't, P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C498440">BSN protein, human</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D002352">Carrier Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009419">Nerve Tissue Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009707">Nucleosomes</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.21.1</RegistryNumber><NameOfSubstance UI="D003850">Deoxyribonuclease I</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020132" MajorTopicYN="N">Anticipation, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002352" MajorTopicYN="N">Carrier Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="Y">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003850" MajorTopicYN="N">Deoxyribonuclease I</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D030342" MajorTopicYN="N">Genetic Diseases, Inborn</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008957" MajorTopicYN="Y">Models, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019578" MajorTopicYN="N">Multiple System Atrophy</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009419" MajorTopicYN="N">Nerve Tissue Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009690" MajorTopicYN="N">Nucleic Acid Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009707" MajorTopicYN="N">Nucleosomes</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018583" MajorTopicYN="N">Pliability</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011485" MajorTopicYN="N">Protein Binding</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019680" MajorTopicYN="N">Trinucleotide Repeat Expansion</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018911" MajorTopicYN="N">Trinucleotide Repeats</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2000</Year><Month>4</Month><Day>1</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2000</Year><Month>6</Month><Day>8</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2000</Year><Month>4</Month><Day>1</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">10743558</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/15.11.918</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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