G+C content dominates intrinsic nucleosome occupancy
Identifieur interne : 000727 ( Ncbi/Curation ); précédent : 000726; suivant : 000728G+C content dominates intrinsic nucleosome occupancy
Auteurs : Desiree Tillo [Canada] ; Timothy R. Hughes [Canada]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2009.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- 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
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
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.
Url:
DOI: 10.1186/1471-2105-10-442
PubMed: 20028554
PubMed Central: 2808325
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PMC:2808325Le document en format XML
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<term>Genome</term>
<term>Nucleosomes</term>
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<term>Biologie informatique ()</term>
<term>Composition en bases nucléiques (génétique)</term>
<term>Génome</term>
<term>Nucléosomes</term>
<term>Séquence nucléotidique</term>
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<term>Databases, Genetic</term>
<term>Genome</term>
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<term>Biologie informatique</term>
<term>Génome</term>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>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 <italic>in vitro</italic>
. However, the model is complicated, and it is not clear which specific DNA sequence properties are most important for intrinsic nucleosome-forming preferences.</p>
</sec>
<sec><title>Results</title>
<p>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 <italic>in vitro </italic>
and <italic>in vivo </italic>
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 ~50% of the variation in nucleosome occupancy <italic>in vitro</italic>
.</p>
</sec>
<sec><title>Conclusions</title>
<p>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.</p>
</sec>
</div>
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