High-resolution DNA-binding specificity analysis of yeast transcription factors.
Identifieur interne : 002036 ( PubMed/Corpus ); précédent : 002035; suivant : 002037High-resolution DNA-binding specificity analysis of yeast transcription factors.
Auteurs : Cong Zhu ; Kelsey J R P. Byers ; Rachel Patton Mccord ; Zhenwei Shi ; Michael F. Berger ; Daniel E. Newburger ; Katrina Saulrieta ; Zachary Smith ; Mita V. Shah ; Mathangi Radhakrishnan ; Anthony A. Philippakis ; Yanhui Hu ; Federico De Masi ; Marcin Pacek ; Andreas Rolfs ; Tal Murthy ; Joshua Labaer ; Martha L. BulykSource :
- Genome research [ 1088-9051 ] ; 2009.
English descriptors
- KwdEn :
- Binding Sites, Chromatin Immunoprecipitation, Computational Biology, DNA, Fungal (genetics), DNA, Fungal (metabolism), DNA-Binding Proteins (genetics), DNA-Binding Proteins (metabolism), Gene Expression Profiling, Gene Expression Regulation, Fungal, Genome, Fungal, Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction, Promoter Regions, Genetic, Protein Binding, Regulatory Sequences, Nucleic Acid, Response Elements (genetics), Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins (genetics), Saccharomyces cerevisiae Proteins (metabolism), Transcription Factors (genetics), Transcription Factors (metabolism).
- MESH :
- chemical , genetics : DNA, Fungal, DNA-Binding Proteins, Saccharomyces cerevisiae Proteins, Transcription Factors.
- chemical , metabolism : DNA, Fungal, DNA-Binding Proteins, Saccharomyces cerevisiae Proteins, Transcription Factors.
- genetics : Response Elements.
- Binding Sites, Chromatin Immunoprecipitation, Computational Biology, Gene Expression Profiling, Gene Expression Regulation, Fungal, Genome, Fungal, Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction, Promoter Regions, Genetic, Protein Binding, Regulatory Sequences, Nucleic Acid, Saccharomyces cerevisiae.
Abstract
Transcription factors (TFs) regulate the expression of genes through sequence-specific interactions with DNA-binding sites. However, despite recent progress in identifying in vivo TF binding sites by microarray readout of chromatin immunoprecipitation (ChIP-chip), nearly half of all known yeast TFs are of unknown DNA-binding specificities, and many additional predicted TFs remain uncharacterized. To address these gaps in our knowledge of yeast TFs and their cis regulatory sequences, we have determined high-resolution binding profiles for 89 known and predicted yeast TFs, over more than 2.3 million gapped and ungapped 8-bp sequences ("k-mers"). We report 50 new or significantly different direct DNA-binding site motifs for yeast DNA-binding proteins and motifs for eight proteins for which only a consensus sequence was previously known; in total, this corresponds to over a 50% increase in the number of yeast DNA-binding proteins with experimentally determined DNA-binding specificities. Among other novel regulators, we discovered proteins that bind the PAC (Polymerase A and C) motif (GATGAG) and regulate ribosomal RNA (rRNA) transcription and processing, core cellular processes that are constituent to ribosome biogenesis. In contrast to earlier data types, these comprehensive k-mer binding data permit us to consider the regulatory potential of genomic sequence at the individual word level. These k-mer data allowed us to reannotate in vivo TF binding targets as direct or indirect and to examine TFs' potential effects on gene expression in approximately 1,700 environmental and cellular conditions. These approaches could be adapted to identify TFs and cis regulatory elements in higher eukaryotes.
DOI: 10.1101/gr.090233.108
PubMed: 19158363
Links to Exploration step
pubmed:19158363Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">High-resolution DNA-binding specificity analysis of yeast transcription factors.</title><author><name sortKey="Zhu, Cong" sort="Zhu, Cong" uniqKey="Zhu C" first="Cong" last="Zhu">Cong Zhu</name><affiliation><nlm:affiliation>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Byers, Kelsey J R P" sort="Byers, Kelsey J R P" uniqKey="Byers K" first="Kelsey J R P" last="Byers">Kelsey J R P. Byers</name></author><author><name sortKey="Mccord, Rachel Patton" sort="Mccord, Rachel Patton" uniqKey="Mccord R" first="Rachel Patton" last="Mccord">Rachel Patton Mccord</name></author><author><name sortKey="Shi, Zhenwei" sort="Shi, Zhenwei" uniqKey="Shi Z" first="Zhenwei" last="Shi">Zhenwei Shi</name></author><author><name sortKey="Berger, Michael F" sort="Berger, Michael F" uniqKey="Berger M" first="Michael F" last="Berger">Michael F. Berger</name></author><author><name sortKey="Newburger, Daniel E" sort="Newburger, Daniel E" uniqKey="Newburger D" first="Daniel E" last="Newburger">Daniel E. Newburger</name></author><author><name sortKey="Saulrieta, Katrina" sort="Saulrieta, Katrina" uniqKey="Saulrieta K" first="Katrina" last="Saulrieta">Katrina Saulrieta</name></author><author><name sortKey="Smith, Zachary" sort="Smith, Zachary" uniqKey="Smith Z" first="Zachary" last="Smith">Zachary Smith</name></author><author><name sortKey="Shah, Mita V" sort="Shah, Mita V" uniqKey="Shah M" first="Mita V" last="Shah">Mita V. Shah</name></author><author><name sortKey="Radhakrishnan, Mathangi" sort="Radhakrishnan, Mathangi" uniqKey="Radhakrishnan M" first="Mathangi" last="Radhakrishnan">Mathangi Radhakrishnan</name></author><author><name sortKey="Philippakis, Anthony A" sort="Philippakis, Anthony A" uniqKey="Philippakis A" first="Anthony A" last="Philippakis">Anthony A. Philippakis</name></author><author><name sortKey="Hu, Yanhui" sort="Hu, Yanhui" uniqKey="Hu Y" first="Yanhui" last="Hu">Yanhui Hu</name></author><author><name sortKey="De Masi, Federico" sort="De Masi, Federico" uniqKey="De Masi F" first="Federico" last="De Masi">Federico De Masi</name></author><author><name sortKey="Pacek, Marcin" sort="Pacek, Marcin" uniqKey="Pacek M" first="Marcin" last="Pacek">Marcin Pacek</name></author><author><name sortKey="Rolfs, Andreas" sort="Rolfs, Andreas" uniqKey="Rolfs A" first="Andreas" last="Rolfs">Andreas Rolfs</name></author><author><name sortKey="Murthy, Tal" sort="Murthy, Tal" uniqKey="Murthy T" first="Tal" last="Murthy">Tal Murthy</name></author><author><name sortKey="Labaer, Joshua" sort="Labaer, Joshua" uniqKey="Labaer J" first="Joshua" last="Labaer">Joshua Labaer</name></author><author><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L" last="Bulyk">Martha L. Bulyk</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2009">2009</date><idno type="RBID">pubmed:19158363</idno><idno type="pmid">19158363</idno><idno type="doi">10.1101/gr.090233.108</idno><idno type="wicri:Area/PubMed/Corpus">002036</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002036</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">High-resolution DNA-binding specificity analysis of yeast transcription factors.</title><author><name sortKey="Zhu, Cong" sort="Zhu, Cong" uniqKey="Zhu C" first="Cong" last="Zhu">Cong Zhu</name><affiliation><nlm:affiliation>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Byers, Kelsey J R P" sort="Byers, Kelsey J R P" uniqKey="Byers K" first="Kelsey J R P" last="Byers">Kelsey J R P. Byers</name></author><author><name sortKey="Mccord, Rachel Patton" sort="Mccord, Rachel Patton" uniqKey="Mccord R" first="Rachel Patton" last="Mccord">Rachel Patton Mccord</name></author><author><name sortKey="Shi, Zhenwei" sort="Shi, Zhenwei" uniqKey="Shi Z" first="Zhenwei" last="Shi">Zhenwei Shi</name></author><author><name sortKey="Berger, Michael F" sort="Berger, Michael F" uniqKey="Berger M" first="Michael F" last="Berger">Michael F. Berger</name></author><author><name sortKey="Newburger, Daniel E" sort="Newburger, Daniel E" uniqKey="Newburger D" first="Daniel E" last="Newburger">Daniel E. Newburger</name></author><author><name sortKey="Saulrieta, Katrina" sort="Saulrieta, Katrina" uniqKey="Saulrieta K" first="Katrina" last="Saulrieta">Katrina Saulrieta</name></author><author><name sortKey="Smith, Zachary" sort="Smith, Zachary" uniqKey="Smith Z" first="Zachary" last="Smith">Zachary Smith</name></author><author><name sortKey="Shah, Mita V" sort="Shah, Mita V" uniqKey="Shah M" first="Mita V" last="Shah">Mita V. Shah</name></author><author><name sortKey="Radhakrishnan, Mathangi" sort="Radhakrishnan, Mathangi" uniqKey="Radhakrishnan M" first="Mathangi" last="Radhakrishnan">Mathangi Radhakrishnan</name></author><author><name sortKey="Philippakis, Anthony A" sort="Philippakis, Anthony A" uniqKey="Philippakis A" first="Anthony A" last="Philippakis">Anthony A. Philippakis</name></author><author><name sortKey="Hu, Yanhui" sort="Hu, Yanhui" uniqKey="Hu Y" first="Yanhui" last="Hu">Yanhui Hu</name></author><author><name sortKey="De Masi, Federico" sort="De Masi, Federico" uniqKey="De Masi F" first="Federico" last="De Masi">Federico De Masi</name></author><author><name sortKey="Pacek, Marcin" sort="Pacek, Marcin" uniqKey="Pacek M" first="Marcin" last="Pacek">Marcin Pacek</name></author><author><name sortKey="Rolfs, Andreas" sort="Rolfs, Andreas" uniqKey="Rolfs A" first="Andreas" last="Rolfs">Andreas Rolfs</name></author><author><name sortKey="Murthy, Tal" sort="Murthy, Tal" uniqKey="Murthy T" first="Tal" last="Murthy">Tal Murthy</name></author><author><name sortKey="Labaer, Joshua" sort="Labaer, Joshua" uniqKey="Labaer J" first="Joshua" last="Labaer">Joshua Labaer</name></author><author><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L" last="Bulyk">Martha L. Bulyk</name></author></analytic><series><title level="j">Genome research</title><idno type="ISSN">1088-9051</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites</term><term>Chromatin Immunoprecipitation</term><term>Computational Biology</term><term>DNA, Fungal (genetics)</term><term>DNA, Fungal (metabolism)</term><term>DNA-Binding Proteins (genetics)</term><term>DNA-Binding Proteins (metabolism)</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Fungal</term><term>Genome, Fungal</term><term>Oligonucleotide Array Sequence Analysis</term><term>Polymerase Chain Reaction</term><term>Promoter Regions, Genetic</term><term>Protein Binding</term><term>Regulatory Sequences, Nucleic Acid</term><term>Response Elements (genetics)</term><term>Saccharomyces cerevisiae</term><term>Saccharomyces cerevisiae Proteins (genetics)</term><term>Saccharomyces cerevisiae Proteins (metabolism)</term><term>Transcription Factors (genetics)</term><term>Transcription Factors (metabolism)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Fungal</term><term>DNA-Binding Proteins</term><term>Saccharomyces cerevisiae Proteins</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA, Fungal</term><term>DNA-Binding Proteins</term><term>Saccharomyces cerevisiae Proteins</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Response Elements</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Chromatin Immunoprecipitation</term><term>Computational Biology</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Fungal</term><term>Genome, Fungal</term><term>Oligonucleotide Array Sequence Analysis</term><term>Polymerase Chain Reaction</term><term>Promoter Regions, Genetic</term><term>Protein Binding</term><term>Regulatory Sequences, Nucleic Acid</term><term>Saccharomyces cerevisiae</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Transcription factors (TFs) regulate the expression of genes through sequence-specific interactions with DNA-binding sites. However, despite recent progress in identifying in vivo TF binding sites by microarray readout of chromatin immunoprecipitation (ChIP-chip), nearly half of all known yeast TFs are of unknown DNA-binding specificities, and many additional predicted TFs remain uncharacterized. To address these gaps in our knowledge of yeast TFs and their cis regulatory sequences, we have determined high-resolution binding profiles for 89 known and predicted yeast TFs, over more than 2.3 million gapped and ungapped 8-bp sequences ("k-mers"). We report 50 new or significantly different direct DNA-binding site motifs for yeast DNA-binding proteins and motifs for eight proteins for which only a consensus sequence was previously known; in total, this corresponds to over a 50% increase in the number of yeast DNA-binding proteins with experimentally determined DNA-binding specificities. Among other novel regulators, we discovered proteins that bind the PAC (Polymerase A and C) motif (GATGAG) and regulate ribosomal RNA (rRNA) transcription and processing, core cellular processes that are constituent to ribosome biogenesis. In contrast to earlier data types, these comprehensive k-mer binding data permit us to consider the regulatory potential of genomic sequence at the individual word level. These k-mer data allowed us to reannotate in vivo TF binding targets as direct or indirect and to examine TFs' potential effects on gene expression in approximately 1,700 environmental and cellular conditions. These approaches could be adapted to identify TFs and cis regulatory elements in higher eukaryotes.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19158363</PMID><DateCompleted><Year>2009</Year><Month>05</Month><Day>29</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1088-9051</ISSN><JournalIssue CitedMedium="Print"><Volume>19</Volume><Issue>4</Issue><PubDate><Year>2009</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Genome research</Title><ISOAbbreviation>Genome Res.</ISOAbbreviation></Journal><ArticleTitle>High-resolution DNA-binding specificity analysis of yeast transcription factors.</ArticleTitle><Pagination><MedlinePgn>556-66</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1101/gr.090233.108</ELocationID><Abstract><AbstractText>Transcription factors (TFs) regulate the expression of genes through sequence-specific interactions with DNA-binding sites. However, despite recent progress in identifying in vivo TF binding sites by microarray readout of chromatin immunoprecipitation (ChIP-chip), nearly half of all known yeast TFs are of unknown DNA-binding specificities, and many additional predicted TFs remain uncharacterized. To address these gaps in our knowledge of yeast TFs and their cis regulatory sequences, we have determined high-resolution binding profiles for 89 known and predicted yeast TFs, over more than 2.3 million gapped and ungapped 8-bp sequences ("k-mers"). We report 50 new or significantly different direct DNA-binding site motifs for yeast DNA-binding proteins and motifs for eight proteins for which only a consensus sequence was previously known; in total, this corresponds to over a 50% increase in the number of yeast DNA-binding proteins with experimentally determined DNA-binding specificities. Among other novel regulators, we discovered proteins that bind the PAC (Polymerase A and C) motif (GATGAG) and regulate ribosomal RNA (rRNA) transcription and processing, core cellular processes that are constituent to ribosome biogenesis. In contrast to earlier data types, these comprehensive k-mer binding data permit us to consider the regulatory potential of genomic sequence at the individual word level. These k-mer data allowed us to reannotate in vivo TF binding targets as direct or indirect and to examine TFs' potential effects on gene expression in approximately 1,700 environmental and cellular conditions. These approaches could be adapted to identify TFs and cis regulatory elements in higher eukaryotes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Cong</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Byers</LastName><ForeName>Kelsey J R P</ForeName><Initials>KJ</Initials></Author><Author ValidYN="Y"><LastName>McCord</LastName><ForeName>Rachel Patton</ForeName><Initials>RP</Initials></Author><Author ValidYN="Y"><LastName>Shi</LastName><ForeName>Zhenwei</ForeName><Initials>Z</Initials></Author><Author ValidYN="Y"><LastName>Berger</LastName><ForeName>Michael F</ForeName><Initials>MF</Initials></Author><Author ValidYN="Y"><LastName>Newburger</LastName><ForeName>Daniel E</ForeName><Initials>DE</Initials></Author><Author ValidYN="Y"><LastName>Saulrieta</LastName><ForeName>Katrina</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Smith</LastName><ForeName>Zachary</ForeName><Initials>Z</Initials></Author><Author ValidYN="Y"><LastName>Shah</LastName><ForeName>Mita V</ForeName><Initials>MV</Initials></Author><Author ValidYN="Y"><LastName>Radhakrishnan</LastName><ForeName>Mathangi</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Philippakis</LastName><ForeName>Anthony A</ForeName><Initials>AA</Initials></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Yanhui</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>De Masi</LastName><ForeName>Federico</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Pacek</LastName><ForeName>Marcin</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Rolfs</LastName><ForeName>Andreas</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Murthy</LastName><ForeName>Tal</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Labaer</LastName><ForeName>Joshua</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Bulyk</LastName><ForeName>Martha L</ForeName><Initials>ML</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GEO</DataBankName><AccessionNumberList><AccessionNumber>GSE13684</AccessionNumber></AccessionNumberList></DataBank></DataBankList><GrantList CompleteYN="Y"><Grant><GrantID>R01 HG003985-03</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 HG003985</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 HG003420-02</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 HG003420-03S1</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 HG003420-03</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 HG003420</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2009</Year><Month>01</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Genome Res</MedlineTA><NlmUniqueID>9518021</NlmUniqueID><ISSNLinking>1088-9051</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004271">DNA, Fungal</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004268">DNA-Binding Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D029701">Saccharomyces cerevisiae Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D047369" MajorTopicYN="N">Chromatin Immunoprecipitation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004271" MajorTopicYN="N">DNA, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004268" MajorTopicYN="N">DNA-Binding Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015966" MajorTopicYN="Y">Gene Expression Regulation, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016681" MajorTopicYN="N">Genome, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020411" MajorTopicYN="N">Oligonucleotide Array Sequence Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011401" MajorTopicYN="N">Promoter Regions, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011485" MajorTopicYN="N">Protein Binding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012045" MajorTopicYN="N">Regulatory Sequences, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020218" MajorTopicYN="N">Response Elements</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012441" MajorTopicYN="N">Saccharomyces cerevisiae</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D029701" MajorTopicYN="N">Saccharomyces cerevisiae Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2009</Year><Month>1</Month><Day>23</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2009</Year><Month>1</Month><Day>23</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2009</Year><Month>5</Month><Day>30</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">19158363</ArticleId><ArticleId IdType="pii">gr.090233.108</ArticleId><ArticleId IdType="doi">10.1101/gr.090233.108</ArticleId><ArticleId IdType="pmc">PMC2665775</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Mol Cell. 1999 Nov;4(5):715-23</Citation><ArticleIdList><ArticleId IdType="pubmed">10619019</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biol Chem. 2007 Sep 7;282(36):26623-8</Citation><ArticleIdList><ArticleId IdType="pubmed">17616518</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 2000 Jul 7;102(1):109-26</Citation><ArticleIdList><ArticleId IdType="pubmed">10929718</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Cell. 2000 Dec;11(12):4241-57</Citation><ArticleIdList><ArticleId IdType="pubmed">11102521</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2000 Dec 22;290(5500):2306-9</Citation><ArticleIdList><ArticleId IdType="pubmed">11125145</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2001 Jan 25;409(6819):533-8</Citation><ArticleIdList><ArticleId IdType="pubmed">11206552</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Cell. 2001 Feb;12(2):323-37</Citation><ArticleIdList><ArticleId IdType="pubmed">11179418</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Cell. 2001 Apr;7(4):741-51</Citation><ArticleIdList><ArticleId IdType="pubmed">11336698</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2001 May 4;292(5518):929-34</Citation><ArticleIdList><ArticleId IdType="pubmed">11340206</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2001 Jun 19;98(13):7158-63</Citation><ArticleIdList><ArticleId IdType="pubmed">11404456</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 2001 Aug;28(4):327-34</Citation><ArticleIdList><ArticleId IdType="pubmed">11455386</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 2001 Sep 21;106(6):697-708</Citation><ArticleIdList><ArticleId IdType="pubmed">11572776</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 2001 Oct;29(2):153-9</Citation><ArticleIdList><ArticleId IdType="pubmed">11547334</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2654-9</Citation><ArticleIdList><ArticleId IdType="pubmed">11880620</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Cell. 2002 Mar;9(3):563-73</Citation><ArticleIdList><ArticleId IdType="pubmed">11931764</ArticleId></ArticleIdList></Reference><Reference><Citation>Genes Dev. 2002 Apr 1;16(7):806-19</Citation><ArticleIdList><ArticleId IdType="pubmed">11937489</ArticleId></ArticleIdList></Reference><Reference><Citation>Genes Dev. 2002 Dec 1;16(23):3034-45</Citation><ArticleIdList><ArticleId IdType="pubmed">12464633</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2003 Jan 1;31(1):374-8</Citation><ArticleIdList><ArticleId IdType="pubmed">12520026</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2003 May 15;423(6937):241-54</Citation><ArticleIdList><ArticleId IdType="pubmed">12748633</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2003 Jul 4;301(5629):71-6</Citation><ArticleIdList><ArticleId IdType="pubmed">12775844</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2002 Nov 13;3:35</Citation><ArticleIdList><ArticleId IdType="pubmed">12431279</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2003 Dec 12;19(18):2502-4</Citation><ArticleIdList><ArticleId IdType="pubmed">14668247</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 2004 Apr 16;117(2):185-98</Citation><ArticleIdList><ArticleId IdType="pubmed">15084257</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2004 Sep 2;431(7004):99-104</Citation><ArticleIdList><ArticleId IdType="pubmed">15343339</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biol Chem. 1991 Aug 15;266(23):15300-7</Citation><ArticleIdList><ArticleId IdType="pubmed">1869554</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 1993 Aug 13;261(5123):909-11</Citation><ArticleIdList><ArticleId IdType="pubmed">8346441</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Cell Biol. 1996 Jul;16(7):3773-80</Citation><ArticleIdList><ArticleId IdType="pubmed">8668194</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 1996 Dec 27;87(7):1249-60</Citation><ArticleIdList><ArticleId IdType="pubmed">8980231</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biol Chem. 1998 Jul 17;273(29):18556-61</Citation><ArticleIdList><ArticleId IdType="pubmed">9660826</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 1998 Oct;16(10):939-45</Citation><ArticleIdList><ArticleId IdType="pubmed">9788350</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 1999 Jun;17(6):573-7</Citation><ArticleIdList><ArticleId IdType="pubmed">10385322</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 1999 Jul;22(3):281-5</Citation><ArticleIdList><ArticleId IdType="pubmed">10391217</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 2004 Dec;36(12):1331-9</Citation><ArticleIdList><ArticleId IdType="pubmed">15543148</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Biol. 2004 Dec;2(12):e398</Citation><ArticleIdList><ArticleId IdType="pubmed">15534694</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Biol. 2005 Jan 11;15(1):68-72</Citation><ArticleIdList><ArticleId IdType="pubmed">15649368</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2005;6(2):R16</Citation><ArticleIdList><ArticleId IdType="pubmed">15693945</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>Cell. 2005 Aug 26;122(4):517-27</Citation><ArticleIdList><ArticleId IdType="pubmed">16122420</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 2006 Jan 13;124(1):207-19</Citation><ArticleIdList><ArticleId IdType="pubmed">16413492</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2006 Feb;172(2):795-809</Citation><ArticleIdList><ArticleId IdType="pubmed">16204215</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2006;7:113</Citation><ArticleIdList><ArticleId IdType="pubmed">16522208</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2006 May 19;312(5776):1054-9</Citation><ArticleIdList><ArticleId IdType="pubmed">16709784</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2006 Aug;16(8):962-72</Citation><ArticleIdList><ArticleId IdType="pubmed">16809671</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Protoc Mol Biol. 2005 Feb;Chapter 21:Unit 21.3</Citation><ArticleIdList><ArticleId IdType="pubmed">18265358</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 2008 Jun 27;133(7):1266-76</Citation><ArticleIdList><ArticleId IdType="pubmed">18585359</ArticleId></ArticleIdList></Reference><Reference><Citation>J Comput Biol. 2008 Sep;15(7):655-65</Citation><ArticleIdList><ArticleId IdType="pubmed">18651798</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2009 Jan;37(Database issue):D77-82</Citation><ArticleIdList><ArticleId IdType="pubmed">18842628</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Protoc. 2009;4(3):393-411</Citation><ArticleIdList><ArticleId IdType="pubmed">19265799</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Opin Biotechnol. 2006 Aug;17(4):422-30</Citation><ArticleIdList><ArticleId IdType="pubmed">16839757</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12045-50</Citation><ArticleIdList><ArticleId IdType="pubmed">16880382</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2006 Nov;24(11):1429-35</Citation><ArticleIdList><ArticleId IdType="pubmed">16998473</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2007 Apr;17(4):536-43</Citation><ArticleIdList><ArticleId IdType="pubmed">17322287</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Syst Biol. 2007;3:100</Citation><ArticleIdList><ArticleId IdType="pubmed">17437025</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7068-73</Citation><ArticleIdList><ArticleId IdType="pubmed">17438293</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2007 Jun 8;316(5830):1497-502</Citation><ArticleIdList><ArticleId IdType="pubmed">17540862</ArticleId></ArticleIdList></Reference><Reference><Citation>Funct Integr Genomics. 2007 Oct;7(4):335-45</Citation><ArticleIdList><ArticleId IdType="pubmed">17638031</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Biol. 2000 Mar 10;296(5):1205-14</Citation><ArticleIdList><ArticleId IdType="pubmed">10698627</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002036 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd -nk 002036 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= PubMed
|étape= Corpus
|type= RBID
|clé= pubmed:19158363
|texte= High-resolution DNA-binding specificity analysis of yeast transcription factors.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/RBID.i -Sk "pubmed:19158363" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |