G+C content dominates intrinsic nucleosome occupancy
<p>Abstract</p> <p>Background</p> <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 dinucleotid...
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| Format: | Article |
| Language: | English |
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BMC
2009-12-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/10/442 |
| _version_ | 1818150369268596736 |
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| author | Hughes Timothy R Tillo Desiree |
| author_facet | Hughes Timothy R Tillo Desiree |
| author_sort | Hughes Timothy R |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <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 <it>in vitro</it>. However, the model is complicated, and it is not clear which specific DNA sequence properties are most important for intrinsic nucleosome-forming preferences.</p> <p>Results</p> <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 <it>in vitro </it>and <it>in vivo </it>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 <it>in vitro</it>.</p> <p>Conclusions</p> <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> |
| first_indexed | 2024-12-11T13:21:50Z |
| format | Article |
| id | doaj.art-a06f090b6899438883edd66a02f73bc5 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-11T13:21:50Z |
| publishDate | 2009-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-a06f090b6899438883edd66a02f73bc52022-12-22T01:05:46ZengBMCBMC Bioinformatics1471-21052009-12-0110144210.1186/1471-2105-10-442G+C content dominates intrinsic nucleosome occupancyHughes Timothy RTillo Desiree<p>Abstract</p> <p>Background</p> <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 <it>in vitro</it>. However, the model is complicated, and it is not clear which specific DNA sequence properties are most important for intrinsic nucleosome-forming preferences.</p> <p>Results</p> <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 <it>in vitro </it>and <it>in vivo </it>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 <it>in vitro</it>.</p> <p>Conclusions</p> <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>http://www.biomedcentral.com/1471-2105/10/442 |
| spellingShingle | Hughes Timothy R Tillo Desiree G+C content dominates intrinsic nucleosome occupancy BMC Bioinformatics |
| title | G+C content dominates intrinsic nucleosome occupancy |
| title_full | G+C content dominates intrinsic nucleosome occupancy |
| title_fullStr | G+C content dominates intrinsic nucleosome occupancy |
| title_full_unstemmed | G+C content dominates intrinsic nucleosome occupancy |
| title_short | G+C content dominates intrinsic nucleosome occupancy |
| title_sort | g c content dominates intrinsic nucleosome occupancy |
| url | http://www.biomedcentral.com/1471-2105/10/442 |
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