Studying the evolution of promoter sequences: a waiting time problem.
Identifieur interne : 001E16 ( PubMed/Checkpoint ); précédent : 001E15; suivant : 001E17Studying the evolution of promoter sequences: a waiting time problem.
Auteurs : Sarah Behrens [Allemagne] ; Martin VingronSource :
- Journal of computational biology : a journal of computational molecular cell biology [ 1557-8666 ] ; 2010.
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Abstract
To gain a better understanding of the evolutionary dynamics of regulatory DNA sequences, we address the following questions: (1) How long does it take until a given transcription factor (TF) binding site emerges at random in a promoter sequence? and (2) How does the composition of a TF binding site affect this waiting time? Using two different probabilistic models (an i.i.d. model and a neighbor dependent model), we can compute the expected waiting time for every k-mer, k ranging from 5 to 10, until it appears in a promoter of a species. Our findings indicate that new TF binding sites can be created on a short evolutionary time scale, i.e. in a time span below the speciation time of human and chimp. Furthermore, one can conclude that the composition of a TF binding site plays a crucial role concerning the waiting time until it appears and that the CpG methylation-deamination substitution process probably accelerates the creation of new TF binding sites. A screening of existing TF binding sites moreover reveals that k-mers predicted to have short waiting times occur more frequently than others. Supplementary Material is available at www.libertonline.com/cmb .
DOI: 10.1089/cmb.2010.0084
PubMed: 21128851
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troglodytes</term><term>Régions promotrices (génétique)</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Binding Sites</term><term>Databases, Nucleic Acid</term><term>Evolution, Molecular</term><term>Humans</term><term>Models, Genetic</term><term>Molecular Sequence Data</term><term>Time Factors</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Bases de données d'acides nucléiques</term><term>Données de séquences moléculaires</term><term>Facteurs de transcription</term><term>Facteurs temps</term><term>Humains</term><term>Modèles génétiques</term><term>Sites de fixation</term><term>Séquence nucléotidique</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">To gain a better understanding of the evolutionary dynamics of regulatory DNA sequences, we address the following questions: (1) How long does it take until a given transcription factor (TF) binding site emerges at random in a promoter sequence? and (2) How does the composition of a TF binding site affect this waiting time? Using two different probabilistic models (an i.i.d. model and a neighbor dependent model), we can compute the expected waiting time for every k-mer, k ranging from 5 to 10, until it appears in a promoter of a species. Our findings indicate that new TF binding sites can be created on a short evolutionary time scale, i.e. in a time span below the speciation time of human and chimp. Furthermore, one can conclude that the composition of a TF binding site plays a crucial role concerning the waiting time until it appears and that the CpG methylation-deamination substitution process probably accelerates the creation of new TF binding sites. A screening of existing TF binding sites moreover reveals that k-mers predicted to have short waiting times occur more frequently than others. Supplementary Material is available at www.libertonline.com/cmb .</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21128851</PMID><DateCompleted><Year>2011</Year><Month>06</Month><Day>10</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1557-8666</ISSN><JournalIssue CitedMedium="Internet"><Volume>17</Volume><Issue>12</Issue><PubDate><Year>2010</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Journal of computational biology : a journal of computational molecular cell biology</Title><ISOAbbreviation>J. Comput. Biol.</ISOAbbreviation></Journal><ArticleTitle>Studying the evolution of promoter sequences: a waiting time problem.</ArticleTitle><Pagination><MedlinePgn>1591-606</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1089/cmb.2010.0084</ELocationID><Abstract><AbstractText>To gain a better understanding of the evolutionary dynamics of regulatory DNA sequences, we address the following questions: (1) How long does it take until a given transcription factor (TF) binding site emerges at random in a promoter sequence? and (2) How does the composition of a TF binding site affect this waiting time? Using two different probabilistic models (an i.i.d. model and a neighbor dependent model), we can compute the expected waiting time for every k-mer, k ranging from 5 to 10, until it appears in a promoter of a species. Our findings indicate that new TF binding sites can be created on a short evolutionary time scale, i.e. in a time span below the speciation time of human and chimp. Furthermore, one can conclude that the composition of a TF binding site plays a crucial role concerning the waiting time until it appears and that the CpG methylation-deamination substitution process probably accelerates the creation of new TF binding sites. A screening of existing TF binding sites moreover reveals that k-mers predicted to have short waiting times occur more frequently than others. 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IdType="pubmed">10607619</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Allemagne</li></country><region><li>Berlin</li></region><settlement><li>Berlin</li></settlement></list><tree><noCountry><name sortKey="Vingron, Martin" sort="Vingron, Martin" uniqKey="Vingron M" first="Martin" last="Vingron">Martin Vingron</name></noCountry><country name="Allemagne"><region name="Berlin"><name sortKey="Behrens, Sarah" sort="Behrens, Sarah" uniqKey="Behrens S" first="Sarah" last="Behrens">Sarah Behrens</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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