Comparative genomics of Drosophila and human core promoters
Identifieur interne : 000560 ( Pmc/Curation ); précédent : 000559; suivant : 000561Comparative genomics of Drosophila and human core promoters
Auteurs : Peter C. Fitzgerald [États-Unis] ; David Sturgill [États-Unis] ; Andrey Shyakhtenko [États-Unis] ; Brian Oliver [États-Unis] ; Charles Vinson [États-Unis]Source :
- Genome Biology [ 1465-6906 ] ; 2006.
Abstract
Comparison of DNA sequence distributions in
Url:
DOI: 10.1186/gb-2006-7-7-r53
PubMed: 16827941
PubMed Central: 1779564
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Fitzgerald</name><affiliation wicri:level="1"><nlm:aff id="I1">Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892</wicri:regionArea></affiliation></author><author><name sortKey="Sturgill, David" sort="Sturgill, David" uniqKey="Sturgill D" first="David" last="Sturgill">David Sturgill</name><affiliation wicri:level="1"><nlm:aff id="I2">Laboratory of Cellular and Developmental Biology National Institute of Diabetes and Digestive and Kidney, National Institutes of Health, Bethesda, MD 20892, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Laboratory of Cellular and Developmental Biology National Institute of Diabetes and Digestive and Kidney, National Institutes of Health, Bethesda, MD 20892</wicri:regionArea></affiliation></author><author><name sortKey="Shyakhtenko, Andrey" sort="Shyakhtenko, Andrey" uniqKey="Shyakhtenko A" first="Andrey" last="Shyakhtenko">Andrey Shyakhtenko</name><affiliation wicri:level="1"><nlm:aff id="I3">Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892</wicri:regionArea></affiliation></author><author><name sortKey="Oliver, Brian" sort="Oliver, Brian" uniqKey="Oliver B" first="Brian" last="Oliver">Brian Oliver</name><affiliation wicri:level="1"><nlm:aff id="I2">Laboratory of Cellular and Developmental Biology National Institute of Diabetes and Digestive and Kidney, National Institutes of Health, Bethesda, MD 20892, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Laboratory of Cellular and Developmental Biology National Institute of Diabetes and Digestive and Kidney, National Institutes of Health, Bethesda, MD 20892</wicri:regionArea></affiliation></author><author><name sortKey="Vinson, Charles" sort="Vinson, Charles" uniqKey="Vinson C" first="Charles" last="Vinson">Charles Vinson</name><affiliation wicri:level="1"><nlm:aff id="I3">Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">16827941</idno><idno type="pmc">1779564</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779564</idno><idno type="RBID">PMC:1779564</idno><idno type="doi">10.1186/gb-2006-7-7-r53</idno><date when="2006">2006</date><idno type="wicri:Area/Pmc/Corpus">000560</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000560</idno><idno type="wicri:Area/Pmc/Curation">000560</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000560</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comparative genomics of <italic>Drosophila </italic>and human core promoters</title><author><name sortKey="Fitzgerald, Peter C" sort="Fitzgerald, Peter C" uniqKey="Fitzgerald P" first="Peter C" last="Fitzgerald">Peter C. Fitzgerald</name><affiliation wicri:level="1"><nlm:aff id="I1">Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892</wicri:regionArea></affiliation></author><author><name sortKey="Sturgill, David" sort="Sturgill, David" uniqKey="Sturgill D" first="David" last="Sturgill">David Sturgill</name><affiliation wicri:level="1"><nlm:aff id="I2">Laboratory of Cellular and Developmental Biology National Institute of Diabetes and Digestive and Kidney, National Institutes of Health, Bethesda, MD 20892, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Laboratory of Cellular and Developmental Biology National Institute of Diabetes and Digestive and Kidney, National Institutes of Health, Bethesda, MD 20892</wicri:regionArea></affiliation></author><author><name sortKey="Shyakhtenko, Andrey" sort="Shyakhtenko, Andrey" uniqKey="Shyakhtenko A" first="Andrey" last="Shyakhtenko">Andrey Shyakhtenko</name><affiliation wicri:level="1"><nlm:aff id="I3">Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892</wicri:regionArea></affiliation></author><author><name sortKey="Oliver, Brian" sort="Oliver, Brian" uniqKey="Oliver B" first="Brian" last="Oliver">Brian Oliver</name><affiliation wicri:level="1"><nlm:aff id="I2">Laboratory of Cellular and Developmental Biology National Institute of Diabetes and Digestive and Kidney, National Institutes of Health, Bethesda, MD 20892, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Laboratory of Cellular and Developmental Biology National Institute of Diabetes and Digestive and Kidney, National Institutes of Health, Bethesda, MD 20892</wicri:regionArea></affiliation></author><author><name sortKey="Vinson, Charles" sort="Vinson, Charles" uniqKey="Vinson C" first="Charles" last="Vinson">Charles Vinson</name><affiliation wicri:level="1"><nlm:aff id="I3">Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892</wicri:regionArea></affiliation></author></analytic><series><title level="j">Genome Biology</title><idno type="ISSN">1465-6906</idno><idno type="eISSN">1465-6914</idno><imprint><date when="2006">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Comparison of DNA sequence distributions in <italic>Drosophila </italic>and human promoters suggests that different motifs have distinct functional roles.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Biol</journal-id><journal-title>Genome Biology</journal-title><issn pub-type="ppub">1465-6906</issn><issn pub-type="epub">1465-6914</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">16827941</article-id><article-id pub-id-type="pmc">1779564</article-id><article-id pub-id-type="publisher-id">gb-2006-7-7-r53</article-id><article-id pub-id-type="doi">10.1186/gb-2006-7-7-r53</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research</subject></subj-group></article-categories><title-group><article-title>Comparative genomics of <italic>Drosophila </italic>and human core promoters</article-title></title-group><contrib-group><contrib id="A1" contrib-type="author"><name><surname>FitzGerald</surname><given-names>Peter C</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>pcf@helix.nih.gov</email></contrib><contrib id="A2" contrib-type="author"><name><surname>Sturgill</surname><given-names>David</given-names></name><xref ref-type="aff" rid="I2">2</xref><email>sturgill@helix.nih.gov</email></contrib><contrib id="A3" contrib-type="author"><name><surname>Shyakhtenko</surname><given-names>Andrey</given-names></name><xref ref-type="aff" rid="I3">3</xref><email>shlyakha@mail.nih.gov</email></contrib><contrib id="A4" contrib-type="author"><name><surname>Oliver</surname><given-names>Brian</given-names></name><xref ref-type="aff" rid="I2">2</xref><email>oliver@helix.nih.gov</email></contrib><contrib id="A5" corresp="yes" contrib-type="author"><name><surname>Vinson</surname><given-names>Charles</given-names></name><xref ref-type="aff" rid="I3">3</xref><email>vinsonc@dc37a.nci.nih.gov</email></contrib></contrib-group><aff id="I1"><label>1</label>Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA</aff><aff id="I2"><label>2</label>Laboratory of Cellular and Developmental Biology National Institute of Diabetes and Digestive and Kidney, National Institutes of Health, Bethesda, MD 20892, USA</aff><aff id="I3"><label>3</label>Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA</aff><pub-date pub-type="ppub"><year>2006</year></pub-date><pub-date pub-type="epub"><day>7</day><month>7</month><year>2006</year></pub-date><volume>7</volume><issue>7</issue><fpage>R53</fpage><lpage>R53</lpage><ext-link ext-link-type="uri" xlink:href="http://genomebiology.com/2006/7/7/R53"></ext-link><history><date date-type="received"><day>22</day><month>3</month><year>2006</year></date><date date-type="rev-recd"><day>8</day><month>5</month><year>2006</year></date><date date-type="accepted"><day>6</day><month>6</month><year>2006</year></date></history><permissions><copyright-statement>Copyright © 2006 FitzGerald et al.; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2006</copyright-year><copyright-holder>FitzGerald et al.; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><p>This is an open access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0"></ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p><pmc-comment>
FitzGerald
C
Peter
pcf@helix.nih.gov
Comparative genomics of Drosophila and human core promoters
2006 Genome Biology 7(7): R53-. (2006) 1465-6906(2006)7:7 urn:ISSN:1465-6906
</license></permissions><abstract abstract-type="short"><p>Comparison of DNA sequence distributions in <italic>Drosophila </italic>and human promoters suggests that different motifs have distinct functional roles.</p></abstract><abstract><sec><title>Background</title><p>The core promoter region plays a critical role in the regulation of eukaryotic gene expression. We have determined the non-random distribution of DNA sequences relative to the transcriptional start site in <italic>Drosophila melanogaster </italic>promoters to identify sequences that may be biologically significant. We compare these results with those obtained for human promoters.</p></sec><sec><title>Results</title><p>We determined the distribution of all 65,536 octamer (8-mers) DNA sequences in 10,914 <italic>Drosophila </italic>promoters and two sets of human promoters aligned relative to the transcriptional start site. In <italic>Drosophila</italic>, 298 8-mers have highly significant (<italic>p </italic>≤ 1 × 10<sup>-16</sup>) non-random distributions peaking within 100 base-pairs of the transcriptional start site. These sequences were grouped into 15 DNA motifs. Ten motifs, termed directional motifs, occur only on the positive strand while the remaining five motifs, termed non-directional motifs, occur on both strands. The only directional motifs to localize in human promoters are TATA, INR, and DPE. The directional motifs were further subdivided into those precisely positioned relative to the transcriptional start site and those that are positioned more loosely relative to the transcriptional start site. Similar numbers of non-directional motifs were identified in both species and most are different. The genes associated with all 15 DNA motifs, when they occur in the peak, are enriched in specific Gene Ontology categories and show a distinct mRNA expression pattern, suggesting that there is a core promoter code in <italic>Drosophila</italic>.</p></sec><sec><title>Conclusion</title><p><italic>Drosophila </italic>and human promoters use different DNA sequences to regulate gene expression, supporting the idea that evolution occurs by the modulation of gene regulation.</p></sec></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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