DNA sequence symmetries from randomness: the origin of the Chargaff's second parity rule.
Identifieur interne : 000070 ( PubMed/Curation ); précédent : 000069; suivant : 000071DNA sequence symmetries from randomness: the origin of the Chargaff's second parity rule.
Auteurs : Piero Fariselli [Italie] ; Cristian Taccioli [Italie] ; Luca Pagani [Italie] ; Amos Maritan [Italie]Source :
- Briefings in bioinformatics [ 1477-4054 ] ; 2020.
Abstract
Most living organisms rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered as the main target of evolution. However, here we show that symmetries and patterns in the dsDNA sequence can emerge from the physical peculiarities of the dsDNA molecule itself and the maximum entropy principle alone, rather than from biological or environmental evolutionary pressure. The randomness justifies the human codon biases and context-dependent mutation patterns in human populations. Thus, the DNA 'exceptional symmetries,' emerged from the randomness, have to be taken into account when looking for the DNA encoded information. Our results suggest that the double helix energy constraints and, more generally, the physical properties of the dsDNA are the hard drivers of the overall DNA sequence architecture, whereas the selective biological processes act as soft drivers, which only under extraordinary circumstances overtake the overall entropy content of the genome.
DOI: 10.1093/bib/bbaa041
PubMed: 32266404
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000070
Links to Exploration step
pubmed:32266404Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">DNA sequence symmetries from randomness: the origin of the Chargaff's second parity rule.</title>
<author><name sortKey="Fariselli, Piero" sort="Fariselli, Piero" uniqKey="Fariselli P" first="Piero" last="Fariselli">Piero Fariselli</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Medical Sciences of the University of Turin, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Department of Medical Sciences of the University of Turin</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Taccioli, Cristian" sort="Taccioli, Cristian" uniqKey="Taccioli C" first="Cristian" last="Taccioli">Cristian Taccioli</name>
<affiliation wicri:level="1"><nlm:affiliation>MAPS Department at the University of Padova, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>MAPS Department at the University of Padova</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Pagani, Luca" sort="Pagani, Luca" uniqKey="Pagani L" first="Luca" last="Pagani">Luca Pagani</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Biology of the University of Padova, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Department of Biology of the University of Padova</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Maritan, Amos" sort="Maritan, Amos" uniqKey="Maritan A" first="Amos" last="Maritan">Amos Maritan</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Physics of the University of Padova, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Department of Physics of the University of Padova</wicri:regionArea>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2020">2020</date>
<idno type="RBID">pubmed:32266404</idno>
<idno type="pmid">32266404</idno>
<idno type="doi">10.1093/bib/bbaa041</idno>
<idno type="wicri:Area/PubMed/Corpus">000070</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000070</idno>
<idno type="wicri:Area/PubMed/Curation">000070</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000070</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">DNA sequence symmetries from randomness: the origin of the Chargaff's second parity rule.</title>
<author><name sortKey="Fariselli, Piero" sort="Fariselli, Piero" uniqKey="Fariselli P" first="Piero" last="Fariselli">Piero Fariselli</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Medical Sciences of the University of Turin, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Department of Medical Sciences of the University of Turin</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Taccioli, Cristian" sort="Taccioli, Cristian" uniqKey="Taccioli C" first="Cristian" last="Taccioli">Cristian Taccioli</name>
<affiliation wicri:level="1"><nlm:affiliation>MAPS Department at the University of Padova, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>MAPS Department at the University of Padova</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Pagani, Luca" sort="Pagani, Luca" uniqKey="Pagani L" first="Luca" last="Pagani">Luca Pagani</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Biology of the University of Padova, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Department of Biology of the University of Padova</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Maritan, Amos" sort="Maritan, Amos" uniqKey="Maritan A" first="Amos" last="Maritan">Amos Maritan</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Physics of the University of Padova, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Department of Physics of the University of Padova</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series><title level="j">Briefings in bioinformatics</title>
<idno type="eISSN">1477-4054</idno>
<imprint><date when="2020" type="published">2020</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Most living organisms rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered as the main target of evolution. However, here we show that symmetries and patterns in the dsDNA sequence can emerge from the physical peculiarities of the dsDNA molecule itself and the maximum entropy principle alone, rather than from biological or environmental evolutionary pressure. The randomness justifies the human codon biases and context-dependent mutation patterns in human populations. Thus, the DNA 'exceptional symmetries,' emerged from the randomness, have to be taken into account when looking for the DNA encoded information. Our results suggest that the double helix energy constraints and, more generally, the physical properties of the dsDNA are the hard drivers of the overall DNA sequence architecture, whereas the selective biological processes act as soft drivers, which only under extraordinary circumstances overtake the overall entropy content of the genome.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32266404</PMID>
<DateRevised><Year>2020</Year>
<Month>04</Month>
<Day>08</Day>
</DateRevised>
<Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1477-4054</ISSN>
<JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year>
<Month>Apr</Month>
<Day>08</Day>
</PubDate>
</JournalIssue>
<Title>Briefings in bioinformatics</Title>
<ISOAbbreviation>Brief. Bioinformatics</ISOAbbreviation>
</Journal>
<ArticleTitle>DNA sequence symmetries from randomness: the origin of the Chargaff's second parity rule.</ArticleTitle>
<ELocationID EIdType="pii" ValidYN="Y">bbaa041</ELocationID>
<ELocationID EIdType="doi" ValidYN="Y">10.1093/bib/bbaa041</ELocationID>
<Abstract><AbstractText>Most living organisms rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered as the main target of evolution. However, here we show that symmetries and patterns in the dsDNA sequence can emerge from the physical peculiarities of the dsDNA molecule itself and the maximum entropy principle alone, rather than from biological or environmental evolutionary pressure. The randomness justifies the human codon biases and context-dependent mutation patterns in human populations. Thus, the DNA 'exceptional symmetries,' emerged from the randomness, have to be taken into account when looking for the DNA encoded information. Our results suggest that the double helix energy constraints and, more generally, the physical properties of the dsDNA are the hard drivers of the overall DNA sequence architecture, whereas the selective biological processes act as soft drivers, which only under extraordinary circumstances overtake the overall entropy content of the genome.</AbstractText>
<CopyrightInformation>© The Author(s) 2020. Published by Oxford University Press.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Fariselli</LastName>
<ForeName>Piero</ForeName>
<Initials>P</Initials>
<AffiliationInfo><Affiliation>Department of Medical Sciences of the University of Turin, Italy.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Taccioli</LastName>
<ForeName>Cristian</ForeName>
<Initials>C</Initials>
<AffiliationInfo><Affiliation>MAPS Department at the University of Padova, Italy.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Pagani</LastName>
<ForeName>Luca</ForeName>
<Initials>L</Initials>
<AffiliationInfo><Affiliation>Department of Biology of the University of Padova, Italy.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Maritan</LastName>
<ForeName>Amos</ForeName>
<Initials>A</Initials>
<AffiliationInfo><Affiliation>Department of Physics of the University of Padova, Italy.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2020</Year>
<Month>04</Month>
<Day>08</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>Brief Bioinform</MedlineTA>
<NlmUniqueID>100912837</NlmUniqueID>
<ISSNLinking>1467-5463</ISSNLinking>
</MedlineJournalInfo>
<CitationSubset>IM</CitationSubset>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Chargaff's second parity rule</Keyword>
<Keyword MajorTopicYN="N">DNA k-mers</Keyword>
<Keyword MajorTopicYN="N">DNA symmetries</Keyword>
<Keyword MajorTopicYN="N">codon usage</Keyword>
<Keyword MajorTopicYN="N">genome evolution</Keyword>
<Keyword MajorTopicYN="N">sequence analysis</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year>
<Month>12</Month>
<Day>04</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="revised"><Year>2020</Year>
<Month>02</Month>
<Day>27</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2020</Year>
<Month>03</Month>
<Day>05</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2020</Year>
<Month>4</Month>
<Day>9</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2020</Year>
<Month>4</Month>
<Day>9</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2020</Year>
<Month>4</Month>
<Day>9</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>aheadofprint</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">32266404</ArticleId>
<ArticleId IdType="pii">5817481</ArticleId>
<ArticleId IdType="doi">10.1093/bib/bbaa041</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000070 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd -nk 000070 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= PubMed |étape= Curation |type= RBID |clé= pubmed:32266404 |texte= DNA sequence symmetries from randomness: the origin of the Chargaff's second parity rule. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Curation/RBID.i -Sk "pubmed:32266404" \ | HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
This area was generated with Dilib version V0.6.33. |