Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation
<p>Abstract</p> <p>Background</p> <p>The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence of a motif but also motif...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2008-11-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/9/484 |
| _version_ | 1818021718664413184 |
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| author | Ronne Hans Xu Feifei Westholm Jakub Komorowski Jan |
| author_facet | Ronne Hans Xu Feifei Westholm Jakub Komorowski Jan |
| author_sort | Ronne Hans |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence of a motif but also motif context (for example the orientation of a motif or its location relative to the coding sequence) is important for gene regulation.</p> <p>Results</p> <p>In this study we present ContextFinder, a tool that is specifically aimed at identifying cases where motif context is likely to affect gene regulation. We used ContextFinder to examine the role of motif context in <it>S. cerevisiae </it>both for DNA binding by transcription factors and for effects on gene expression. For DNA binding we found significant patterns of motif location bias, whereas motif orientations did not seem to matter. Motif context appears to affect gene expression even more than it affects DNA binding, as biases in both motif location and orientation were more frequent in promoters of co-expressed genes. We validated our results against data on nucleosome positioning, and found a negative correlation between preferred motif locations and nucleosome occupancy.</p> <p>Conclusion</p> <p>We conclude that the requirement for stable binding of transcription factors to DNA and their subsequent function in gene regulation can impose constraints on motif context.</p> |
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| format | Article |
| id | doaj.art-03088006314b44a1bb609c7a844ba735 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-14T08:21:41Z |
| publishDate | 2008-11-01 |
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| spelling | doaj.art-03088006314b44a1bb609c7a844ba7352022-12-22T02:04:11ZengBMCBMC Bioinformatics1471-21052008-11-019148410.1186/1471-2105-9-484Genome-scale study of the importance of binding site context for transcription factor binding and gene regulationRonne HansXu FeifeiWestholm JakubKomorowski Jan<p>Abstract</p> <p>Background</p> <p>The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence of a motif but also motif context (for example the orientation of a motif or its location relative to the coding sequence) is important for gene regulation.</p> <p>Results</p> <p>In this study we present ContextFinder, a tool that is specifically aimed at identifying cases where motif context is likely to affect gene regulation. We used ContextFinder to examine the role of motif context in <it>S. cerevisiae </it>both for DNA binding by transcription factors and for effects on gene expression. For DNA binding we found significant patterns of motif location bias, whereas motif orientations did not seem to matter. Motif context appears to affect gene expression even more than it affects DNA binding, as biases in both motif location and orientation were more frequent in promoters of co-expressed genes. We validated our results against data on nucleosome positioning, and found a negative correlation between preferred motif locations and nucleosome occupancy.</p> <p>Conclusion</p> <p>We conclude that the requirement for stable binding of transcription factors to DNA and their subsequent function in gene regulation can impose constraints on motif context.</p>http://www.biomedcentral.com/1471-2105/9/484 |
| spellingShingle | Ronne Hans Xu Feifei Westholm Jakub Komorowski Jan Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation BMC Bioinformatics |
| title | Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation |
| title_full | Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation |
| title_fullStr | Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation |
| title_full_unstemmed | Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation |
| title_short | Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation |
| title_sort | genome scale study of the importance of binding site context for transcription factor binding and gene regulation |
| url | http://www.biomedcentral.com/1471-2105/9/484 |
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