Comparative genomics of Drosophila and human core promoters.
Identifieur interne : 002150 ( PubMed/Checkpoint ); précédent : 002149; suivant : 002151Comparative genomics of Drosophila and human core promoters.
Auteurs : Peter C. Fitzgerald [États-Unis] ; David Sturgill ; Andrey Shyakhtenko ; Brian Oliver ; Charles VinsonSource :
- Genome biology [ 1474-760X ] ; 2006.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA, Messenger.
- genetics : Drosophila melanogaster.
- Animals, Genomics, Humans, Promoter Regions, Genetic, Transcription, Genetic.
Abstract
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 Drosophila melanogaster promoters to identify sequences that may be biologically significant. We compare these results with those obtained for human promoters.
DOI: 10.1186/gb-2006-7-7-r53
PubMed: 16827941
Affiliations:
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Fitzgerald</name><affiliation wicri:level="2"><nlm:affiliation>Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Sturgill, David" sort="Sturgill, David" uniqKey="Sturgill D" first="David" last="Sturgill">David Sturgill</name></author><author><name sortKey="Shyakhtenko, Andrey" sort="Shyakhtenko, Andrey" uniqKey="Shyakhtenko A" first="Andrey" last="Shyakhtenko">Andrey Shyakhtenko</name></author><author><name sortKey="Oliver, Brian" sort="Oliver, Brian" uniqKey="Oliver B" first="Brian" last="Oliver">Brian Oliver</name></author><author><name sortKey="Vinson, Charles" sort="Vinson, Charles" uniqKey="Vinson C" first="Charles" last="Vinson">Charles Vinson</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:16827941</idno><idno type="pmid">16827941</idno><idno type="doi">10.1186/gb-2006-7-7-r53</idno><idno type="wicri:Area/PubMed/Corpus">002244</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002244</idno><idno type="wicri:Area/PubMed/Curation">002244</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002244</idno><idno type="wicri:Area/PubMed/Checkpoint">002150</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002150</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Comparative genomics of Drosophila 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="2"><nlm:affiliation>Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Sturgill, David" sort="Sturgill, David" uniqKey="Sturgill D" first="David" last="Sturgill">David Sturgill</name></author><author><name sortKey="Shyakhtenko, Andrey" sort="Shyakhtenko, Andrey" uniqKey="Shyakhtenko A" first="Andrey" last="Shyakhtenko">Andrey Shyakhtenko</name></author><author><name sortKey="Oliver, Brian" sort="Oliver, Brian" uniqKey="Oliver B" first="Brian" last="Oliver">Brian Oliver</name></author><author><name sortKey="Vinson, Charles" sort="Vinson, Charles" uniqKey="Vinson C" first="Charles" last="Vinson">Charles Vinson</name></author></analytic><series><title level="j">Genome biology</title><idno type="eISSN">1474-760X</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Drosophila melanogaster (genetics)</term><term>Genomics</term><term>Humans</term><term>Promoter Regions, Genetic</term><term>RNA, Messenger (genetics)</term><term>Transcription, Genetic</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN messager (génétique)</term><term>Animaux</term><term>Drosophila melanogaster (génétique)</term><term>Génomique</term><term>Humains</term><term>Régions promotrices (génétique)</term><term>Transcription génétique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Messenger</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Drosophila melanogaster</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN messager</term><term>Drosophila melanogaster</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Genomics</term><term>Humans</term><term>Promoter Regions, Genetic</term><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Génomique</term><term>Humains</term><term>Régions promotrices (génétique)</term><term>Transcription génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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 Drosophila melanogaster promoters to identify sequences that may be biologically significant. We compare these results with those obtained for human promoters.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16827941</PMID><DateCompleted><Year>2007</Year><Month>05</Month><Day>31</Day></DateCompleted><DateRevised><Year>2019</Year><Month>10</Month><Day>03</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1474-760X</ISSN><JournalIssue CitedMedium="Internet"><Volume>7</Volume><Issue>7</Issue><PubDate><Year>2006</Year></PubDate></JournalIssue><Title>Genome biology</Title><ISOAbbreviation>Genome Biol.</ISOAbbreviation></Journal><ArticleTitle>Comparative genomics of Drosophila and human core promoters.</ArticleTitle><Pagination><MedlinePgn>R53</MedlinePgn></Pagination><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">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 Drosophila melanogaster promoters to identify sequences that may be biologically significant. We compare these results with those obtained for human promoters.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We determined the distribution of all 65,536 octamer (8-mers) DNA sequences in 10,914 Drosophila promoters and two sets of human promoters aligned relative to the transcriptional start site. In Drosophila, 298 8-mers have highly significant (p < or = 1 x 10(-16)) 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 Drosophila.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">Drosophila and human promoters use different DNA sequences to regulate gene expression, supporting the idea that evolution occurs by the modulation of gene regulation.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>FitzGerald</LastName><ForeName>Peter C</ForeName><Initials>PC</Initials><AffiliationInfo><Affiliation>Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sturgill</LastName><ForeName>David</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Shyakhtenko</LastName><ForeName>Andrey</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Oliver</LastName><ForeName>Brian</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Vinson</LastName><ForeName>Charles</ForeName><Initials>C</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>Z01 DK015600-12</GrantID><Agency>Intramural NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052060">Research Support, N.I.H., Intramural</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Genome 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IdType="pubmed">16827941</ArticleId><ArticleId IdType="pii">gb-2006-7-7-r53</ArticleId><ArticleId IdType="doi">10.1186/gb-2006-7-7-r53</ArticleId><ArticleId IdType="pmc">PMC1779564</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Dev Biol. 2005 Jul 15;283(2):486-502</Citation><ArticleIdList><ArticleId IdType="pubmed">15927177</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2005 May 17;102(20):7203-8</Citation><ArticleIdList><ArticleId IdType="pubmed">15883364</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2005 Sep 16;309(5742):1850-4</Citation><ArticleIdList><ArticleId IdType="pubmed">16141373</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 2005 Oct;37(10):1090-7</Citation><ArticleIdList><ArticleId IdType="pubmed">16155569</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2006 Jan 1;34(Database issue):D86-9</Citation><ArticleIdList><ArticleId IdType="pubmed">16381981</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc IEEE Comput Syst Bioinform Conf. 2004;:425-35</Citation><ArticleIdList><ArticleId IdType="pubmed">16448035</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2000 Mar 15;28(6):1439-46</Citation><ArticleIdList><ArticleId IdType="pubmed">10684940</ArticleId></ArticleIdList></Reference><Reference><Citation>Trends Genet. 2000 Jun;16(6):276-7</Citation><ArticleIdList><ArticleId IdType="pubmed">10827456</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Cell Biol. 2000 Jul;20(13):4754-64</Citation><ArticleIdList><ArticleId IdType="pubmed">10848601</ArticleId></ArticleIdList></Reference><Reference><Citation>Development. 2001 May;128(9):1671-86</Citation><ArticleIdList><ArticleId IdType="pubmed">11290304</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2002 Aug;12(8):1190-200</Citation><ArticleIdList><ArticleId IdType="pubmed">12176927</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2003 Jan 1;31(1):51-4</Citation><ArticleIdList><ArticleId IdType="pubmed">12519945</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2002;3(12):RESEARCH0087</Citation><ArticleIdList><ArticleId IdType="pubmed">12537576</ArticleId></ArticleIdList></Reference><Reference><Citation>Novartis Found Symp. 2002;247:66-80; discussion 80-3, 84-90, 244-52</Citation><ArticleIdList><ArticleId IdType="pubmed">12539950</ArticleId></ArticleIdList></Reference><Reference><Citation>Genes Dev. 2003 Jun 1;17(11):1309-20</Citation><ArticleIdList><ArticleId IdType="pubmed">12782648</ArticleId></ArticleIdList></Reference><Reference><Citation>Annu Rev Biochem. 2003;72:449-79</Citation><ArticleIdList><ArticleId IdType="pubmed">12651739</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2002;3:8</Citation><ArticleIdList><ArticleId IdType="pubmed">11882250</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2004 Jun;14(6):1188-90</Citation><ArticleIdList><ArticleId IdType="pubmed">15173120</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2004;5(6):R40</Citation><ArticleIdList><ArticleId IdType="pubmed">15186491</ArticleId></ArticleIdList></Reference><Reference><Citation>Genes Dev. 2004 Jul 1;18(13):1606-17</Citation><ArticleIdList><ArticleId IdType="pubmed">15231738</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biol. 2002;1(1):5</Citation><ArticleIdList><ArticleId IdType="pubmed">12144710</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2004 Aug;14(8):1562-74</Citation><ArticleIdList><ArticleId IdType="pubmed">15256515</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2004;5(10):R80</Citation><ArticleIdList><ArticleId IdType="pubmed">15461798</ArticleId></ArticleIdList></Reference><Reference><Citation>Development. 2004 Nov;131(21):5297-308</Citation><ArticleIdList><ArticleId IdType="pubmed">15456720</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Microbiol. 2004 Nov;54(3):692-701</Citation><ArticleIdList><ArticleId IdType="pubmed">15491360</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 1980 Mar;77(3):1432-6</Citation><ArticleIdList><ArticleId IdType="pubmed">6929494</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 1980 Sep 19;209(4463):1406-14</Citation><ArticleIdList><ArticleId IdType="pubmed">6251548</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 1990 Oct 25;18(20):6097-100</Citation><ArticleIdList><ArticleId IdType="pubmed">2172928</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Opin Genet Dev. 1991 Oct;1(3):330-5</Citation><ArticleIdList><ArticleId IdType="pubmed">1840889</ArticleId></ArticleIdList></Reference><Reference><Citation>Cold Spring Harb Symp Quant Biol. 1993;58:281-5</Citation><ArticleIdList><ArticleId IdType="pubmed">7956040</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 1997 Sep 1;25(17):3389-402</Citation><ArticleIdList><ArticleId IdType="pubmed">9254694</ArticleId></ArticleIdList></Reference><Reference><Citation>Mech Dev. 1998 Nov;78(1-2):125-34</Citation><ArticleIdList><ArticleId IdType="pubmed">9858707</ArticleId></ArticleIdList></Reference><Reference><Citation>J Cell Biochem. 2005 Feb 1;94(2):257-65</Citation><ArticleIdList><ArticleId IdType="pubmed">15546139</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2005 Jan;169(1):161-72</Citation><ArticleIdList><ArticleId IdType="pubmed">15371353</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 2005 Jan 28;120(2):169-81</Citation><ArticleIdList><ArticleId IdType="pubmed">15680324</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2005 Mar 17;434(7031):338-45</Citation><ArticleIdList><ArticleId IdType="pubmed">15735639</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Evol Biol. 2005;5:15</Citation><ArticleIdList><ArticleId IdType="pubmed">15707503</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Cell Biol. 2005 May;25(9):3401-10</Citation><ArticleIdList><ArticleId IdType="pubmed">15831447</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2005 Jul 22;309(5734):626-30</Citation><ArticleIdList><ArticleId IdType="pubmed">15961632</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Maryland</li></region></list><tree><noCountry><name sortKey="Oliver, Brian" sort="Oliver, Brian" uniqKey="Oliver B" first="Brian" last="Oliver">Brian Oliver</name><name sortKey="Shyakhtenko, Andrey" sort="Shyakhtenko, Andrey" uniqKey="Shyakhtenko A" first="Andrey" last="Shyakhtenko">Andrey Shyakhtenko</name><name sortKey="Sturgill, David" sort="Sturgill, David" uniqKey="Sturgill D" first="David" last="Sturgill">David Sturgill</name><name sortKey="Vinson, Charles" sort="Vinson, Charles" uniqKey="Vinson C" first="Charles" last="Vinson">Charles Vinson</name></noCountry><country name="États-Unis"><region name="Maryland"><name sortKey="Fitzgerald, Peter C" sort="Fitzgerald, Peter C" uniqKey="Fitzgerald P" first="Peter C" last="Fitzgerald">Peter C. 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