MersV1, PubMed, Corpus, bibRecord, 001F79

G+C content dominates intrinsic nucleosome occupancy.

Identifieur interne : 001F79 ( PubMed/Corpus ); précédent : 001F78; suivant : 001F80

G+C content dominates intrinsic nucleosome occupancy.

Auteurs : Desiree Tillo ; Timothy R. Hughes

Source :

BMC bioinformatics [ 1471-2105 ] ; 2009.

RBID : pubmed:20028554

English descriptors

KwdEn :
- Base Composition (genetics), Base Sequence, Computational Biology (methods), Databases, Genetic, Genome, Nucleosomes.
MESH :
- chemical : Nucleosomes.
- genetics : Base Composition.
- methods : Computational Biology.
- Base Sequence, Databases, Genetic, Genome.

Abstract

The relative preference of nucleosomes to form on individual DNA sequences plays a major role in genome packaging. A wide variety of DNA sequence features are believed to influence nucleosome formation, including periodic dinucleotide signals, poly-A stretches and other short motifs, and sequence properties that influence DNA structure, including base content. It was recently shown by Kaplan et al. that a probabilistic model using composition of all 5-mers within a nucleosome-sized tiling window accurately predicts intrinsic nucleosome occupancy across an entire genome in vitro. However, the model is complicated, and it is not clear which specific DNA sequence properties are most important for intrinsic nucleosome-forming preferences.

DOI: 10.1186/1471-2105-10-442
PubMed: 20028554

Links to Exploration step

pubmed:20028554

Le document en format XML

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<author><name sortKey="Tillo, Desiree" sort="Tillo, Desiree" uniqKey="Tillo D" first="Desiree" last="Tillo">Desiree Tillo</name>
<affiliation><nlm:affiliation>Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada. desiree.tillo@utoronto.ca</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Hughes, Timothy R" sort="Hughes, Timothy R" uniqKey="Hughes T" first="Timothy R" last="Hughes">Timothy R. Hughes</name>
</author>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">G+C content dominates intrinsic nucleosome occupancy.</title>
<author><name sortKey="Tillo, Desiree" sort="Tillo, Desiree" uniqKey="Tillo D" first="Desiree" last="Tillo">Desiree Tillo</name>
<affiliation><nlm:affiliation>Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada. desiree.tillo@utoronto.ca</nlm:affiliation>
</affiliation>
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<author><name sortKey="Hughes, Timothy R" sort="Hughes, Timothy R" uniqKey="Hughes T" first="Timothy R" last="Hughes">Timothy R. Hughes</name>
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<series><title level="j">BMC bioinformatics</title>
<idno type="eISSN">1471-2105</idno>
<imprint><date when="2009" type="published">2009</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Composition (genetics)</term>
<term>Base Sequence</term>
<term>Computational Biology (methods)</term>
<term>Databases, Genetic</term>
<term>Genome</term>
<term>Nucleosomes</term>
</keywords>
<keywords scheme="MESH" type="chemical" xml:lang="en"><term>Nucleosomes</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Base Composition</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term>
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<keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term>
<term>Databases, Genetic</term>
<term>Genome</term>
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<front><div type="abstract" xml:lang="en">The relative preference of nucleosomes to form on individual DNA sequences plays a major role in genome packaging. A wide variety of DNA sequence features are believed to influence nucleosome formation, including periodic dinucleotide signals, poly-A stretches and other short motifs, and sequence properties that influence DNA structure, including base content. It was recently shown by Kaplan et al. that a probabilistic model using composition of all 5-mers within a nucleosome-sized tiling window accurately predicts intrinsic nucleosome occupancy across an entire genome in vitro. However, the model is complicated, and it is not clear which specific DNA sequence properties are most important for intrinsic nucleosome-forming preferences.</div>
</front>
</TEI>
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<DateCompleted><Year>2010</Year>
<Month>04</Month>
<Day>09</Day>
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<DateRevised><Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
</DateRevised>
<Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2105</ISSN>
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<PubDate><Year>2009</Year>
<Month>Dec</Month>
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<Title>BMC bioinformatics</Title>
<ISOAbbreviation>BMC Bioinformatics</ISOAbbreviation>
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<ArticleTitle>G+C content dominates intrinsic nucleosome occupancy.</ArticleTitle>
<Pagination><MedlinePgn>442</MedlinePgn>
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<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The relative preference of nucleosomes to form on individual DNA sequences plays a major role in genome packaging. A wide variety of DNA sequence features are believed to influence nucleosome formation, including periodic dinucleotide signals, poly-A stretches and other short motifs, and sequence properties that influence DNA structure, including base content. It was recently shown by Kaplan et al. that a probabilistic model using composition of all 5-mers within a nucleosome-sized tiling window accurately predicts intrinsic nucleosome occupancy across an entire genome in vitro. However, the model is complicated, and it is not clear which specific DNA sequence properties are most important for intrinsic nucleosome-forming preferences.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">We find that a simple linear combination of only 14 simple DNA sequence attributes (G+C content, two transformations of dinucleotide composition, and the frequency of eleven 4-bp sequences) explains nucleosome occupancy in vitro and in vivo in a manner comparable to the Kaplan model. G+C content and frequency of AAAA are the most important features. G+C content is dominant, alone explaining approximately 50% of the variation in nucleosome occupancy in vitro.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Our findings provide a dramatically simplified means to predict and understand intrinsic nucleosome occupancy. G+C content may dominate because it both reduces frequency of poly-A-like stretches and correlates with many other DNA structural characteristics. Since G+C content is enriched or depleted at many types of features in diverse eukaryotic genomes, our results suggest that variation in nucleotide composition may have a widespread and direct influence on chromatin structure.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tillo</LastName>
<ForeName>Desiree</ForeName>
<Initials>D</Initials>
<AffiliationInfo><Affiliation>Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada. desiree.tillo@utoronto.ca</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Hughes</LastName>
<ForeName>Timothy R</ForeName>
<Initials>TR</Initials>
</Author>
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<Language>eng</Language>
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<Month>12</Month>
<Day>22</Day>
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G+C content dominates intrinsic nucleosome occupancy.

G+C content dominates intrinsic nucleosome occupancy.

Source :

English descriptors

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

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