High-resolution DNA-binding specificity analysis of yeast transcription factors.
Identifieur interne : 002789 ( Main/Exploration ); précédent : 002788; suivant : 002790High-resolution DNA-binding specificity analysis of yeast transcription factors.
Auteurs : Cong Zhu [États-Unis] ; 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.
Descripteurs français
- KwdFr :
- ADN fongique (génétique), ADN fongique (métabolisme), Analyse de profil d'expression de gènes, Biologie informatique, Facteurs de transcription (génétique), Facteurs de transcription (métabolisme), Génome fongique, Immunoprécipitation de la chromatine, Liaison aux protéines, Protéines de Saccharomyces cerevisiae (génétique), Protéines de Saccharomyces cerevisiae (métabolisme), Protéines de liaison à l'ADN (génétique), Protéines de liaison à l'ADN (métabolisme), Réaction de polymérisation en chaîne, Régions promotrices (génétique), Régulation de l'expression des gènes fongiques, Saccharomyces cerevisiae, Sites de fixation, Séquences d'acides nucléiques régulatrices, Séquençage par oligonucléotides en batterie, Éléments de réponse (génétique).
- MESH :
- génétique : ADN fongique, Facteurs de transcription, Protéines de Saccharomyces cerevisiae, Protéines de liaison à l'ADN, Éléments de réponse.
- métabolisme : ADN fongique, Facteurs de transcription, Protéines de Saccharomyces cerevisiae, Protéines de liaison à l'ADN.
- Analyse de profil d'expression de gènes, Biologie informatique, Génome fongique, Immunoprécipitation de la chromatine, Liaison aux protéines, Réaction de polymérisation en chaîne, Régions promotrices (génétique), Régulation de l'expression des gènes fongiques, Saccharomyces cerevisiae, Sites de fixation, Séquences d'acides nucléiques régulatrices, Séquençage par oligonucléotides en batterie.
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
Affiliations:
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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="KwdFr" xml:lang="fr"><term>ADN fongique (génétique)</term><term>ADN fongique (métabolisme)</term><term>Analyse de profil d'expression de gènes</term><term>Biologie informatique</term><term>Facteurs de transcription (génétique)</term><term>Facteurs de transcription (métabolisme)</term><term>Génome fongique</term><term>Immunoprécipitation de la chromatine</term><term>Liaison aux protéines</term><term>Protéines de Saccharomyces cerevisiae (génétique)</term><term>Protéines de Saccharomyces cerevisiae (métabolisme)</term><term>Protéines de liaison à l'ADN (génétique)</term><term>Protéines de liaison à l'ADN (métabolisme)</term><term>Réaction de polymérisation en chaîne</term><term>Régions promotrices (génétique)</term><term>Régulation de l'expression des gènes fongiques</term><term>Saccharomyces cerevisiae</term><term>Sites de fixation</term><term>Séquences d'acides nucléiques régulatrices</term><term>Séquençage par oligonucléotides en batterie</term><term>Éléments de réponse (génétique)</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" qualifier="génétique" xml:lang="fr"><term>ADN fongique</term><term>Facteurs de transcription</term><term>Protéines de Saccharomyces cerevisiae</term><term>Protéines de liaison à l'ADN</term><term>Éléments de réponse</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN fongique</term><term>Facteurs de transcription</term><term>Protéines de Saccharomyces cerevisiae</term><term>Protéines de liaison à l'ADN</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><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Biologie informatique</term><term>Génome fongique</term><term>Immunoprécipitation de la chromatine</term><term>Liaison aux protéines</term><term>Réaction de polymérisation en chaîne</term><term>Régions promotrices (génétique)</term><term>Régulation de l'expression des gènes fongiques</term><term>Saccharomyces cerevisiae</term><term>Sites de fixation</term><term>Séquences d'acides nucléiques régulatrices</term><term>Séquençage par oligonucléotides en batterie</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><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Berger, Michael F" sort="Berger, Michael F" uniqKey="Berger M" first="Michael F" last="Berger">Michael F. Berger</name><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L" last="Bulyk">Martha L. Bulyk</name><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><name sortKey="De Masi, Federico" sort="De Masi, Federico" uniqKey="De Masi F" first="Federico" last="De Masi">Federico De Masi</name><name sortKey="Hu, Yanhui" sort="Hu, Yanhui" uniqKey="Hu Y" first="Yanhui" last="Hu">Yanhui Hu</name><name sortKey="Labaer, Joshua" sort="Labaer, Joshua" uniqKey="Labaer J" first="Joshua" last="Labaer">Joshua Labaer</name><name sortKey="Mccord, Rachel Patton" sort="Mccord, Rachel Patton" uniqKey="Mccord R" first="Rachel Patton" last="Mccord">Rachel Patton Mccord</name><name sortKey="Murthy, Tal" sort="Murthy, Tal" uniqKey="Murthy T" first="Tal" last="Murthy">Tal Murthy</name><name sortKey="Newburger, Daniel E" sort="Newburger, Daniel E" uniqKey="Newburger D" first="Daniel E" last="Newburger">Daniel E. Newburger</name><name sortKey="Pacek, Marcin" sort="Pacek, Marcin" uniqKey="Pacek M" first="Marcin" last="Pacek">Marcin Pacek</name><name sortKey="Philippakis, Anthony A" sort="Philippakis, Anthony A" uniqKey="Philippakis A" first="Anthony A" last="Philippakis">Anthony A. Philippakis</name><name sortKey="Radhakrishnan, Mathangi" sort="Radhakrishnan, Mathangi" uniqKey="Radhakrishnan M" first="Mathangi" last="Radhakrishnan">Mathangi Radhakrishnan</name><name sortKey="Rolfs, Andreas" sort="Rolfs, Andreas" uniqKey="Rolfs A" first="Andreas" last="Rolfs">Andreas Rolfs</name><name sortKey="Saulrieta, Katrina" sort="Saulrieta, Katrina" uniqKey="Saulrieta K" first="Katrina" last="Saulrieta">Katrina Saulrieta</name><name sortKey="Shah, Mita V" sort="Shah, Mita V" uniqKey="Shah M" first="Mita V" last="Shah">Mita V. Shah</name><name sortKey="Shi, Zhenwei" sort="Shi, Zhenwei" uniqKey="Shi Z" first="Zhenwei" last="Shi">Zhenwei Shi</name><name sortKey="Smith, Zachary" sort="Smith, Zachary" uniqKey="Smith Z" first="Zachary" last="Smith">Zachary Smith</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Zhu, Cong" sort="Zhu, Cong" uniqKey="Zhu C" first="Cong" last="Zhu">Cong Zhu</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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